sbuild (Debian sbuild) 0.79.1 (22 April 2020) on carme.larted.org.uk +==============================================================================+ | apbs 3.0.0+dfsg1-3 (amd64) Fri, 02 Oct 2020 23:32:48 +0000 | +==============================================================================+ Package: apbs Version: 3.0.0+dfsg1-3 Source Version: 3.0.0+dfsg1-3 Distribution: sid Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-debomatic-afdf0e21-5158-4e97-977e-b7c1bc10fdca' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup apbs_3.0.0+dfsg1-3 sid amd64 --------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup apbs_3.0.0+dfsg1-3 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/apbs-biHgNS/resolver-TmDczs' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [146 kB] Get:2 http://localhost:3142/debian sid InRelease [146 kB] Get:3 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-02-0800.55.pdiff [2416 B] Get:5 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-02-1400.49.pdiff [10.2 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-02-2000.55.pdiff [5353 B] Get:6 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-02-2000.55.pdiff [5353 B] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [27.9 kB] Get:8 http://localhost:3142/debian sid/main Sources 2020-10-02-0800.55.pdiff [2429 B] Get:9 http://localhost:3142/debian sid/main Sources 2020-10-02-1400.49.pdiff [9442 B] Get:10 http://localhost:3142/debian sid/main Sources 2020-10-02-2000.55.pdiff [7669 B] Get:10 http://localhost:3142/debian sid/main Sources 2020-10-02-2000.55.pdiff [7669 B] Fetched 386 kB in 3s (150 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/apbs_3.0.0+dfsg1-3.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/apbs-biHgNS/apbs-3.0.0+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/apbs-biHgNS' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), dh-python, libmaloc-dev, mpi-default-dev, python3, python3-dev, python3-setuptools, swig, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: cmake, debhelper-compat (= 13), dh-python, libmaloc-dev, mpi-default-dev, python3, python3-dev, python3-setuptools, swig, zlib1g-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [425 B] Get:5 copy:/<>/apt_archive ./ Packages [510 B] Fetched 1892 B in 0s (29.5 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils build-essential cmake cmake-data cpp-9 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dpkg-dev dwz fakeroot file g++ g++-10 gcc gcc-10 gcc-9 gettext gettext-base gfortran-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libasan5 libasan6 libbrotli1 libbsd0 libc6-dev libcbor0 libcroco3 libcrypt-dev libcurl4 libdebhelper-perl libdpkg-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgcc-10-dev libgcc-9-dev libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmaloc-dev libmaloc1 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libperl5.30 libpipeline1 libpmix-dev libpmix2 libprocps8 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libssh2-1 libssl1.1 libstdc++-10-dev libsub-override-perl libtool libubsan1 libuchardet0 libucx0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db mime-support mpi-default-dev node-jquery ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client perl perl-modules-5.30 po-debconf procps python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.8 python3.8-dev python3.8-minimal sensible-utils swig swig4.0 zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build gcc-9-locales dh-make debian-keyring g++-multilib g++-10-multilib gcc-10-doc gcc-multilib manpages-dev flex bison gdb gcc-doc gcc-10-multilib gcc-10-locales gcc-9-multilib gcc-9-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-9-multilib gfortran-9-doc libcoarrays-dev groff lrzip glibc-doc git bzr krb5-doc krb5-user libhwloc-contrib-plugins libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils libstdc++-10-doc gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc python3.8-venv python3.8-doc binfmt-support swig-doc swig-examples swig4.0-examples swig4.0-doc Recommended packages: libalgorithm-merge-perl curl | wget | lynx ca-certificates libfile-fcntllock-perl liblocale-gettext-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libgpm2 libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils build-essential cmake cmake-data cpp-9 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dpkg-dev dwz fakeroot file g++ g++-10 gcc gcc-10 gcc-9 gettext gettext-base gfortran-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libasan5 libasan6 libbrotli1 libbsd0 libc6-dev libcbor0 libcroco3 libcrypt-dev libcurl4 libdebhelper-perl libdpkg-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgcc-10-dev libgcc-9-dev libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmaloc-dev libmaloc1 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libperl5.30 libpipeline1 libpmix-dev libpmix2 libprocps8 libpsl5 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libssh2-1 libssl1.1 libstdc++-10-dev libsub-override-perl libtool libubsan1 libuchardet0 libucx0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db mime-support mpi-default-dev node-jquery ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client perl perl-modules-5.30 po-debconf procps python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.8 python3.8-dev python3.8-minimal sbuild-build-depends-main-dummy sensible-utils swig swig4.0 zlib1g-dev 0 upgraded, 154 newly installed, 0 to remove and 0 not upgraded. Need to get 134 MB of archives. After this operation, 533 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B] Get:2 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.36-3+b1 [140 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.9.3-2 [1314 kB] Get:7 http://localhost:3142/debian unstable/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB] Get:9 http://localhost:3142/debian unstable/main amd64 perl amd64 5.30.3-4 [290 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libpython3.8-minimal amd64 3.8.6-1 [761 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:13 http://localhost:3142/debian unstable/main amd64 python3.8-minimal amd64 3.8.6-1 [1863 kB] Get:14 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.8.2-3 [37.6 kB] Get:15 http://localhost:3142/debian unstable/main amd64 mime-support all 3.64 [37.8 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libpython3.8-stdlib amd64 3.8.6-1 [1720 kB] Get:17 http://localhost:3142/debian unstable/main amd64 python3.8 amd64 3.8.6-1 [422 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libpython3-stdlib amd64 3.8.2-3 [20.8 kB] Get:19 http://localhost:3142/debian unstable/main amd64 python3 amd64 3.8.2-3 [63.7 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libncurses6 amd64 6.2+20200918-1 [102 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libprocps8 amd64 2:3.3.16-5 [62.7 kB] Get:22 http://localhost:3142/debian unstable/main amd64 procps amd64 2:3.3.16-5 [262 kB] Get:23 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:26 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:27 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libcbor0 amd64 0.5.0+dfsg-2 [24.0 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libfido2-1 amd64 1.5.0-2 [52.3 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.17-10 [64.6 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.17-10 [115 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.17-10 [366 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-10 [156 kB] Get:37 http://localhost:3142/debian unstable/main amd64 openssh-client amd64 1:8.3p1-1 [910 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:39 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:40 http://localhost:3142/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:41 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:42 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.2-4 [801 kB] Get:43 http://localhost:3142/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:44 http://localhost:3142/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.17-1 [104 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libc6-dev amd64 2.31-3 [2395 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libasan6 amd64 10.2.0-13 [340 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libubsan1 amd64 10.2.0-13 [134 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libgcc-10-dev amd64 10.2.0-13 [2327 kB] Get:49 http://localhost:3142/debian unstable/main amd64 gcc-10 amd64 10.2.0-13 [15.9 MB] Get:50 http://localhost:3142/debian unstable/main amd64 gcc amd64 4:10.2.0-1 [5196 B] Get:51 http://localhost:3142/debian unstable/main amd64 libstdc++-10-dev amd64 10.2.0-13 [1738 kB] Get:52 http://localhost:3142/debian unstable/main amd64 g++-10 amd64 10.2.0-13 [8670 kB] Get:53 http://localhost:3142/debian unstable/main amd64 g++ amd64 4:10.2.0-1 [1644 B] Get:54 http://localhost:3142/debian unstable/main amd64 libdpkg-perl all 1.20.5 [1473 kB] Get:55 http://localhost:3142/debian unstable/main amd64 dpkg-dev all 1.20.5 [1909 kB] Get:56 http://localhost:3142/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:57 http://localhost:3142/debian unstable/main amd64 cmake-data all 3.18.2-1 [1725 kB] Get:58 http://localhost:3142/debian unstable/main amd64 libicu67 amd64 67.1-4 [8624 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-6 [692 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libarchive13 amd64 3.4.3-2 [342 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.0.9-2 [287 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.41.0-3 [74.0 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libpsl5 amd64 0.21.0-1.1 [55.3 kB] Get:64 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:65 http://localhost:3142/debian unstable/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libcurl4 amd64 7.72.0-1 [336 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3.1 [77.6 kB] Get:68 http://localhost:3142/debian unstable/main amd64 librhash0 amd64 1.4.0-1 [124 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libuv1 amd64 1.39.0-1 [131 kB] Get:70 http://localhost:3142/debian unstable/main amd64 cmake amd64 3.18.2-1 [5596 kB] Get:71 http://localhost:3142/debian unstable/main amd64 cpp-9 amd64 9.3.0-18 [9712 kB] Get:72 http://localhost:3142/debian unstable/main amd64 libasan5 amd64 9.3.0-18 [390 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libgcc-9-dev amd64 9.3.0-18 [2347 kB] Get:74 http://localhost:3142/debian unstable/main amd64 gcc-9 amd64 9.3.0-18 [10.0 MB] Get:75 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:76 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:77 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.2.1 [188 kB] Get:78 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:79 http://localhost:3142/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB] Get:81 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.9.0-1 [15.2 kB] Get:82 http://localhost:3142/debian unstable/main amd64 libelf1 amd64 0.181-1 [164 kB] Get:83 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:84 http://localhost:3142/debian unstable/main amd64 libglib2.0-0 amd64 2.66.0-2 [1361 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:86 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:87 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:88 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:89 http://localhost:3142/debian unstable/main amd64 debhelper all 13.2.1 [1007 kB] Get:90 http://localhost:3142/debian unstable/main amd64 python3-lib2to3 all 3.8.5-1 [78.4 kB] Get:91 http://localhost:3142/debian unstable/main amd64 python3-distutils all 3.8.5-1 [145 kB] Get:92 http://localhost:3142/debian unstable/main amd64 dh-python all 4.20200925 [98.3 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.25.1-1 [46.8 kB] Get:94 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.25.1-1 [86.8 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libgfortran5 amd64 10.2.0-13 [728 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libgfortran-9-dev amd64 9.3.0-18 [675 kB] Get:97 http://localhost:3142/debian unstable/main amd64 gfortran-9 amd64 9.3.0-18 [10.4 MB] Get:98 http://localhost:3142/debian unstable/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libibverbs1 amd64 31.0-1 [57.2 kB] Get:101 http://localhost:3142/debian unstable/main amd64 ibverbs-providers amd64 31.0-1 [239 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libevent-2.1-7 amd64 2.1.12-stable-1 [188 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get:104 http://localhost:3142/debian unstable/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-1 [110 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-1 [64.1 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-1 [311 kB] Get:108 http://localhost:3142/debian unstable/main amd64 libexpat1-dev amd64 2.2.9-1 [136 kB] Get:109 http://localhost:3142/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6+b1 [169 kB] Get:110 http://localhost:3142/debian unstable/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get:111 http://localhost:3142/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get:112 http://localhost:3142/debian unstable/main amd64 librdmacm1 amd64 31.0-1 [68.1 kB] Get:113 http://localhost:3142/debian unstable/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get:114 http://localhost:3142/debian unstable/main amd64 libhwloc15 amd64 2.3.0+dfsg-1 [145 kB] Get:115 http://localhost:3142/debian unstable/main amd64 libnuma-dev amd64 2.0.12-1+b1 [39.3 kB] Get:116 http://localhost:3142/debian unstable/main amd64 libltdl7 amd64 2.4.6-14 [390 kB] Get:117 http://localhost:3142/debian unstable/main amd64 libltdl-dev amd64 2.4.6-14 [162 kB] Get:118 http://localhost:3142/debian unstable/main amd64 libhwloc-dev amd64 2.3.0+dfsg-1 [223 kB] Get:119 http://localhost:3142/debian unstable/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:122 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.14-2 [139 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.6.12-1 [311 kB] Get:124 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.6.12-1 [770 kB] Get:125 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:126 http://localhost:3142/debian unstable/main amd64 libxnvctrl0 amd64 450.66-1 [26.5 kB] Get:127 http://localhost:3142/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.2.12-4 [37.8 kB] Get:128 http://localhost:3142/debian unstable/main amd64 libhwloc-plugins amd64 2.3.0+dfsg-1 [20.8 kB] Get:129 http://localhost:3142/debian unstable/main amd64 libnl-3-dev amd64 3.4.0-1+b1 [102 kB] Get:130 http://localhost:3142/debian unstable/main amd64 libnl-route-3-dev amd64 3.4.0-1+b1 [176 kB] Get:131 http://localhost:3142/debian unstable/main amd64 libibverbs-dev amd64 31.0-1 [534 kB] Get:132 http://localhost:3142/debian unstable/main amd64 node-jquery all 3.5.1+dfsg-4 [309 kB] Get:133 http://localhost:3142/debian unstable/main amd64 libjs-jquery all 3.5.1+dfsg-4 [3612 B] Get:134 http://localhost:3142/debian unstable/main amd64 libjs-jquery-ui all 1.12.1+dfsg-7 [232 kB] Get:135 http://localhost:3142/debian unstable/main amd64 libmaloc1 amd64 1.5-1 [81.7 kB] Get:136 http://localhost:3142/debian unstable/main amd64 libmaloc-dev amd64 1.5-1 [109 kB] Get:137 http://localhost:3142/debian unstable/main amd64 libpmix2 amd64 3.2.0~rc1-4 [448 kB] Get:138 http://localhost:3142/debian unstable/main amd64 libucx0 amd64 1.9.0~rc1-2 [660 kB] Get:139 http://localhost:3142/debian unstable/main amd64 libopenmpi3 amd64 4.0.5-5 [2166 kB] Get:140 http://localhost:3142/debian unstable/main amd64 openmpi-common all 4.0.5-5 [73.6 kB] Get:141 http://localhost:3142/debian unstable/main amd64 libpmix-dev amd64 3.2.0~rc1-4 [551 kB] Get:142 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:143 http://localhost:3142/debian unstable/main amd64 openmpi-bin amd64 4.0.5-5 [127 kB] Get:144 http://localhost:3142/debian unstable/main amd64 libopenmpi-dev amd64 4.0.5-5 [1090 kB] Get:145 http://localhost:3142/debian unstable/main amd64 libpython3.8 amd64 3.8.6-1 [1608 kB] Get:146 http://localhost:3142/debian unstable/main amd64 libpython3.8-dev amd64 3.8.6-1 [3840 kB] Get:147 http://localhost:3142/debian unstable/main amd64 libpython3-dev amd64 3.8.2-3 [21.0 kB] Get:148 http://localhost:3142/debian unstable/main amd64 mpi-default-dev amd64 1.13 [5476 B] Get:149 http://localhost:3142/debian unstable/main amd64 python3.8-dev amd64 3.8.6-1 [515 kB] Get:150 http://localhost:3142/debian unstable/main amd64 python3-dev amd64 3.8.2-3 [1164 B] Get:151 http://localhost:3142/debian unstable/main amd64 python3-pkg-resources all 49.3.1-2 [188 kB] Get:152 http://localhost:3142/debian unstable/main amd64 python3-setuptools all 49.3.1-2 [512 kB] Get:153 http://localhost:3142/debian unstable/main amd64 swig4.0 amd64 4.0.1-5 [1402 kB] Get:154 http://localhost:3142/debian unstable/main amd64 swig all 4.0.1-5 [329 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 MB in 7s (18.3 MB/s) Selecting previously unselected package bsdextrautils. 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Setting up python3-pkg-resources (49.3.1-2) ... Setting up automake (1:1.16.2-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.5-1) ... Setting up dh-python (4.20200925) ... Setting up gcc-9 (9.3.0-18) ... Setting up libibverbs1:amd64 (31.0-1) ... Setting up gettext (0.19.8.1-10) ... Setting up libstdc++-10-dev:amd64 (10.2.0-13) ... Setting up g++-10 (10.2.0-13) ... Setting up python3-setuptools (49.3.1-2) ... Setting up ibverbs-providers:amd64 (31.0-1) ... Setting up libtool (2.4.6-14) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up openssh-client (1:8.3p1-1) ... Setting up libdebhelper-perl (13.2.1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libgfortran-9-dev:amd64 (9.3.0-18) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gcc (4:10.2.0-1) ... Setting up dpkg-dev (1.20.5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxnvctrl0:amd64 (450.66-1) ... Setting up libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Setting up libltdl-dev:amd64 (2.4.6-14) ... Setting up libjs-jquery-ui (1.12.1+dfsg-7) ... Setting up libpython3.8-dev:amd64 (3.8.6-1) ... Setting up python3.8-dev (3.8.6-1) ... Setting up g++ (4:10.2.0-1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up cmake (3.18.2-1) ... Setting up build-essential (12.8) ... Setting up libhwloc-dev:amd64 (2.3.0+dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up librdmacm1:amd64 (31.0-1) ... Setting up libucx0:amd64 (1.9.0~rc1-2) ... Setting up libpython3-dev:amd64 (3.8.2-3) ... Setting up gfortran-9 (9.3.0-18) ... Setting up po-debconf (1.0.21) ... Setting up libibverbs-dev:amd64 (31.0-1) ... Setting up libhwloc-plugins:amd64 (2.3.0+dfsg-1) ... Setting up python3-dev (3.8.2-3) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:amd64 (3.2.0~rc1-4) ... Setting up libopenmpi3:amd64 (4.0.5-5) ... Setting up libpmix-dev:amd64 (3.2.0~rc1-4) ... Setting up openmpi-bin (4.0.5-5) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.0.5-5) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.13) ... Setting up debhelper (13.2.1) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.7.0-2-amd64 #1 SMP Debian 5.7.10-1 (2020-07-26) amd64 (x86_64) Toolchain package versions: binutils_2.35.1-1 dpkg-dev_1.20.5 g++-10_10.2.0-13 gcc-10_10.2.0-13 gcc-9_9.3.0-18 libc6-dev_2.31-3 libstdc++-10-dev_10.2.0-13 libstdc++6_10.2.0-13 linux-libc-dev_5.8.10-1 Package versions: adduser_3.118 apt_2.1.10 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-7 binutils_2.35.1-1 binutils-common_2.35.1-1 binutils-x86-64-linux-gnu_2.35.1-1 bsdextrautils_2.36-3+b1 bsdutils_1:2.36-3+b1 build-essential_12.8 bzip2_1.0.8-4 cmake_3.18.2-1 cmake-data_3.18.2-1 coreutils_8.32-4+b1 cpp_4:10.2.0-1 cpp-10_10.2.0-13 cpp-7_7.5.0-6 cpp-9_9.3.0-18 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debian-archive-keyring_2019.1 debianutils_4.11.2 dh-autoreconf_19 dh-python_4.20200925 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5 dpkg-dev_1.20.5 dwz_0.13-5 e2fsprogs_1.45.6-1 eatmydata_105-9 fakeroot_1.25.1-1 fdisk_2.36-3+b1 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.2.0-1 g++-10_10.2.0-13 gcc_4:10.2.0-1 gcc-10_10.2.0-13 gcc-10-base_10.2.0-13 gcc-7-base_7.5.0-6 gcc-8-base_8.4.0-4 gcc-9_9.3.0-18 gcc-9-base_9.3.0-18 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran-9_9.3.0-18 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 ibverbs-providers_31.0-1 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan4_7.5.0-6 libasan5_9.3.0-18 libasan6_10.2.0-13 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.35.1-1 libblkid1_2.36-3+b1 libbrotli1_1.0.9-2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-3 libc-dev-bin_2.31-3 libc6_2.31-3 libc6-dev_2.31-3 libcap-ng0_0.7.9-2.2 libcbor0_0.5.0+dfsg-2 libcc1-0_10.2.0-13 libcilkrts5_7.5.0-6 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-1 libctf0_2.35.1-1 libcurl4_7.72.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5 libeatmydata1_105-9 libedit2_3.1-20191231-1 libelf1_0.181-1 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 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libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 libldap-2.4-2_2.4.53+dfsg-1 libldap-common_2.4.53+dfsg-1 liblsan0_10.2.0-13 libltdl-dev_2.4.6-14 libltdl7_2.4.6-14 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmaloc-dev_1.5-1 libmaloc1_1.5-1 libmount1_2.36-3+b1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libmpx2_8.4.0-4 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle6_3.5.1+really3.4.1-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnl-3-200_3.4.0-1+b1 libnl-3-dev_3.4.0-1+b1 libnl-route-3-200_3.4.0-1+b1 libnl-route-3-dev_3.4.0-1+b1 libnpth0_1.6-2 libnuma-dev_2.0.12-1+b1 libnuma1_2.0.12-1+b1 libopenmpi-dev_4.0.5-5 libopenmpi3_4.0.5-5 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.16-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.26_5.26.2-7+b1 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libpmix-dev_3.2.0~rc1-4 libpmix2_3.2.0~rc1-4 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.1 libpsm-infinipath1_3.3+20.604758e7-6+b1 libpsm2-2_11.2.185-1 libpython3-dev_3.8.2-3 libpython3-stdlib_3.8.2-3 libpython3.8_3.8.6-1 libpython3.8-dev_3.8.6-1 libpython3.8-minimal_3.8.6-1 libpython3.8-stdlib_3.8.6-1 libquadmath0_10.2.0-13 librdmacm1_31.0-1 libreadline7_7.0-5 libreadline8_8.0-4 librhash0_1.4.0-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.4-1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3+b1 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-13 libstdc++6_10.2.0-13 libsub-override-perl_0.09-2 libsystemd0_246.6-1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtool_2.4.6-14 libtsan0_10.2.0-13 libubsan0_7.5.0-6 libubsan1_10.2.0-13 libuchardet0_0.0.7-1 libucx0_1.9.0~rc1-2 libudev1_246.6-1 libunistring2_0.9.10-4 libuuid1_2.36-3+b1 libuv1_1.39.0-1 libx11-6_2:1.6.12-1 libx11-data_2:1.6.12-1 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-6 libxnvctrl0_450.66-1 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.10-1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.36-3+b1 mpi-default-dev_1.13 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.1 node-jquery_3.5.1+dfsg-4 ocl-icd-libopencl1_2.2.12-4 openmpi-bin_4.0.5-5 openmpi-common_4.0.5-5 openssh-client_1:8.3p1-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.26_5.26.2-7 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 procps_2:3.3.16-5 python3_3.8.2-3 python3-dev_3.8.2-3 python3-distutils_3.8.5-1 python3-lib2to3_3.8.5-1 python3-minimal_3.8.2-3 python3-pkg-resources_49.3.1-2 python3-setuptools_49.3.1-2 python3.8_3.8.6-1 python3.8-dev_3.8.6-1 python3.8-minimal_3.8.6-1 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 swig_4.0.1-5 swig4.0_4.0.1-5 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3+b1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: apbs Binary: apbs, python3-apbslib, libapbs-dev, libapbs3, apbs-data Architecture: any all Version: 3.0.0+dfsg1-3 Maintainer: Debichem Team Uploaders: Michael Banck Homepage: http://www.poissonboltzmann.org/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/debichem-team/apbs Vcs-Git: https://salsa.debian.org/debichem-team/apbs.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: cmake, debhelper-compat (= 13), dh-python, libmaloc-dev, mpi-default-dev, python3, python3-dev, python3-setuptools, swig, zlib1g-dev Package-List: apbs deb science optional arch=any apbs-data deb science optional arch=all libapbs-dev deb libdevel optional arch=any libapbs3 deb libs optional arch=any python3-apbslib deb python optional arch=any Checksums-Sha1: 976730bac6bbaa26cdef8d0d5be5c1bf3c63240e 90469528 apbs_3.0.0+dfsg1.orig.tar.xz 7fd00c61349ff3e8d4e912871d6b9066b2ef3c50 14280 apbs_3.0.0+dfsg1-3.debian.tar.xz Checksums-Sha256: bbb2b3f7c14773e6c3535a6af6f5ac40370f4fc62e1fb1c2fe7c39051a8cc5cd 90469528 apbs_3.0.0+dfsg1.orig.tar.xz c9573aab7b2d26f4925c82a597bf4658c33dab324a99f245c46247cb8f43ca37 14280 apbs_3.0.0+dfsg1-3.debian.tar.xz Files: 9f14961e11c5da2f3c5e4979ff29a34c 90469528 apbs_3.0.0+dfsg1.orig.tar.xz 6c5ce01351dda9673668ca8af404f631 14280 apbs_3.0.0+dfsg1-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAl8ZZG0ACgkQVz7x5L1a 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check signature: No public key dpkg-source: warning: failed to verify signature on ./apbs_3.0.0+dfsg1-3.dsc dpkg-source: info: extracting apbs in /<> dpkg-source: info: unpacking apbs_3.0.0+dfsg1.orig.tar.xz dpkg-source: info: unpacking apbs_3.0.0+dfsg1-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying wrong-path-for-interpreter.patch dpkg-source: info: applying debian_testfiles.patch dpkg-source: info: applying debian_make.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying shared_library_soname.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying link_libapbs_routines.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network apbs_3.0.0+dfsg1-3 sid amd64 --------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network apbs_3.0.0+dfsg1-3 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus HOME=/sbuild-nonexistent LANG=C LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=sid-amd64-debomatic SCHROOT_CHROOT_NAME=sid-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=112 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=sid-amd64-debomatic-afdf0e21-5158-4e97-977e-b7c1bc10fdca SCHROOT_UID=1001 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic XDG_RUNTIME_DIR=/run/user/1001 XDG_SESSION_CLASS=background XDG_SESSION_ID=c3821058 XDG_SESSION_TYPE=unspecified dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package apbs dpkg-buildpackage: info: source version 3.0.0+dfsg1-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean --sourcedir=apbs make[1]: Leaving directory '/<>' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building apbs using existing ./apbs_3.0.0+dfsg1.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: warning: ignoring deletion of file apbs/examples/hca-bind/UHBD/bindf.out.orig, use --include-removal to override dpkg-source: info: building apbs in apbs_3.0.0+dfsg1-3.debian.tar.xz dpkg-source: info: building apbs in apbs_3.0.0+dfsg1-3.dsc debian/rules build dh build --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure --sourcedir=apbs -- \ -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=On \ -DBUILD_DOC=Off -DBUILD_TOOLS=On \ -DENABLE_OPENMP=On -DENABLE_MPI=On \ -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On \ -DENABLE_READLINE=Off -DENABLE_ZLIB=On \ -DFETK_PATH=/usr -DENABLE_FETK=Off cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=On -DBUILD_DOC=Off -DBUILD_TOOLS=On -DENABLE_OPENMP=On -DENABLE_MPI=On -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On -DENABLE_READLINE=Off -DENABLE_ZLIB=On -DFETK_PATH=/usr -DENABLE_FETK=Off ../apbs CMake Deprecation Warning at CMakeLists.txt:10 (cmake_policy): The OLD behavior for policy CMP0054 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- The C compiler identification is GNU 10.2.0 -- The CXX compiler identification is GNU 10.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Checking for MPI -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI support enabled -- Inline functions enabled -- Verbose debugging mode enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies m;stdc++;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;maloc;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies m;stdc++;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;maloc;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies m;stdc++;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;maloc;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies m;stdc++;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;maloc;-fopenmp -- Added apbs_routines -- External Headers: -- -- APBS Libraries: m;stdc++;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;maloc;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines -- -- -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc -- Found SWIG: /usr/bin/swig4.0 (found version "4.0.1") -- Found Python3: /usr/bin/python3.8 (found version "3.8.6") found components: Interpreter Development Development.Module Development.Embed -- ******* Python3 FOUND -- ***** Python3 include path is: /usr/include/python3.8 -- ***** Python3 library path is: /usr/lib/x86_64-linux-gnu/libpython3.8.so -- ***** Python3 library dir is: /usr/lib/x86_64-linux-gnu -- Found Python3: /usr/bin/python3.8 (found version "3.8.6") found components: Interpreter -- ******* Python3 FOUND /usr/bin/python3.8 -- TEST born_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t born -- TEST actin-dimer-auto_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t actin-dimer-auto -- TEST actin-dimer-parallel_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t actin-dimer-parallel -- TEST alkanes_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t alkanes -- TEST FKBP_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t FKBP -- TEST hca-bind_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t hca-bind -- TEST ionize_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t ionize -- TEST ion-pmf_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t ion-pmf -- TEST pka-lig_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t pka-lig -- TEST point-pmf_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t point-pmf -- TEST solv_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t solv -- TEST protein-rna_test COMMAND /usr/bin/python3.8 /<>/apbs/tests/apbs_tester.py -c /<>/apbs/tests/test_cases.cfg -e /<>/obj-x86_64-linux-gnu/apbs -t protein-rna -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY ENABLE_READLINE ENABLE_ZLIB FETK_PATH -- Build files have been written to: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build --sourcedir=apbs cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/apbs -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/src/pmgc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/pmgc /<>/obj-x86_64-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/src/generic /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/generic /<>/obj-x86_64-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/python /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/python /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake --color= Scanning dependencies of target apbslib_swig_compilation make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Swig compile apbslib.i for python cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /<>/obj-x86_64-linux-gnu/tools/python /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir Scanning dependencies of target apbs_generic Scanning dependencies of target apbs_pmgc make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E touch /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig4.0 -python -outdir /<>/obj-x86_64-linux-gnu/tools/python -interface _apbslib -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -I/usr/include/python3.8 -I/<>/apbs/tools/python -o /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /<>/apbs/tools/python/apbslib.i [ 2%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /<>/apbs/src/pmgc/buildAd.c [ 3%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/nosh.c.o -c /<>/apbs/src/generic/nosh.c [ 4%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /<>/apbs/src/pmgc/buildBd.c make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target apbslib_swig_compilation [ 5%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/buildGd.c.o -c /<>/apbs/src/pmgc/buildGd.c [ 6%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o [ 8%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /<>/apbs/src/pmgc/buildPd.c cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/cgd.c.o -c /<>/apbs/src/pmgc/cgd.c [ 9%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/gsd.c.o -c /<>/apbs/src/pmgc/gsd.c [ 10%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/matvecd.c.o -c /<>/apbs/src/pmgc/matvecd.c [ 11%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/mgparm.c.o -c /<>/apbs/src/generic/mgparm.c [ 12%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -c /<>/apbs/src/pmgc/mgcsd.c [ 13%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/femparm.c.o -c /<>/apbs/src/generic/femparm.c [ 15%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/pbamparm.c.o -c /<>/apbs/src/generic/pbamparm.c [ 16%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /<>/apbs/src/generic/pbsamparm.c [ 17%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /<>/apbs/src/generic/pbeparm.c [ 18%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /<>/apbs/src/pmgc/mgdrvd.c [ 19%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /<>/apbs/src/pmgc/mgsubd.c [ 20%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/bemparm.c.o -c /<>/apbs/src/generic/bemparm.c [ 22%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/geoflowparm.c.o -c /<>/apbs/src/generic/geoflowparm.c [ 23%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c /<>/apbs/src/pmgc/mikpckd.c [ 24%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/apolparm.c.o -c /<>/apbs/src/generic/apolparm.c [ 25%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -c /<>/apbs/src/pmgc/mlinpckd.c [ 26%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mypdec.c.o -c /<>/apbs/src/pmgc/mypdec.c [ 27%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vacc.c.o -c /<>/apbs/src/generic/vacc.c [ 29%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /<>/apbs/src/pmgc/newtond.c [ 30%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /<>/apbs/src/pmgc/newdrvd.c [ 31%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /<>/apbs/src/pmgc/powerd.c [ 32%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /<>/apbs/src/pmgc/smoothd.c [ 33%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /<>/apbs/src/pmgc/mgfasd.c [ 34%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/valist.c.o -c /<>/apbs/src/generic/valist.c [ 36%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vatom.c.o -c /<>/apbs/src/generic/vatom.c [ 37%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vpbe.c.o -c /<>/apbs/src/generic/vpbe.c [ 38%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vcap.c.o -c /<>/apbs/src/generic/vcap.c [ 39%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vclist.c.o -c /<>/apbs/src/generic/vclist.c [ 40%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vstring.c.o -c /<>/apbs/src/generic/vstring.c [ 41%] Linking C shared library ../../lib/libapbs_pmgc.so cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so.3 -o ../../lib/libapbs_pmgc.so.3 CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp [ 43%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vparam.c.o -c /<>/apbs/src/generic/vparam.c [ 44%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_generic.dir/vgreen.c.o -c /<>/apbs/src/generic/vgreen.c cd /<>/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_symlink_library ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_pmgc.so make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 44%] Built target apbs_pmgc [ 45%] Linking C shared library ../../lib/libapbs_generic.so cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so.3 -o ../../lib/libapbs_generic.so.3 CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbamparm.c.o CMakeFiles/apbs_generic.dir/pbsamparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o CMakeFiles/apbs_generic.dir/geoflowparm.c.o CMakeFiles/apbs_generic.dir/apolparm.c.o CMakeFiles/apbs_generic.dir/vacc.c.o CMakeFiles/apbs_generic.dir/valist.c.o CMakeFiles/apbs_generic.dir/vatom.c.o CMakeFiles/apbs_generic.dir/vpbe.c.o CMakeFiles/apbs_generic.dir/vcap.c.o CMakeFiles/apbs_generic.dir/vclist.c.o CMakeFiles/apbs_generic.dir/vstring.c.o CMakeFiles/apbs_generic.dir/vparam.c.o CMakeFiles/apbs_generic.dir/vgreen.c.o -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp cd /<>/obj-x86_64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_symlink_library ../../lib/libapbs_generic.so.3 ../../lib/libapbs_generic.so.3 ../../lib/libapbs_generic.so make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 45%] Built target apbs_generic make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/src/mg /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/mg /<>/obj-x86_64-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake --color= Scanning dependencies of target apbs_mg make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 46%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /<>/apbs/src/mg/vgrid.c [ 47%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o [ 48%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /<>/apbs/src/mg/vmgrid.c cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vopot.c.o -c /<>/apbs/src/mg/vopot.c [ 50%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vpmg.c.o -c /<>/apbs/src/mg/vpmg.c /<>/apbs/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /<>/apbs/src/mg/vgrid.c:853:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /<>/apbs/src/mg/vpmgp.c [ 52%] Linking C shared library ../../lib/libapbs_mg.so cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so.3 -o ../../lib/libapbs_mg.so.3 CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp ../../lib/libapbs_generic.so.3 ../../lib/libapbs_pmgc.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp cd /<>/obj-x86_64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_symlink_library ../../lib/libapbs_mg.so.3 ../../lib/libapbs_mg.so.3 ../../lib/libapbs_mg.so make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 52%] Built target apbs_mg make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src /<>/obj-x86_64-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake --color= make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake --color= Scanning dependencies of target uhbd_asc2bin make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build Scanning dependencies of target apbs_routines make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' Scanning dependencies of target tensor2dx make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' Scanning dependencies of target mgmesh make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 53%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o [ 54%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /<>/apbs/tools/mesh/uhbd_asc2bin.c cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/tensor2dx.dir/tensor2dx.c.o -c /<>/apbs/tools/mesh/tensor2dx.c [ 55%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/apbs_routines.dir/routines.c.o -c /<>/apbs/src/routines.c [ 56%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/mgmesh.dir/mgmesh.c.o -c /<>/apbs/tools/mesh/mgmesh.c /<>/apbs/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /<>/apbs/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c: In function ‘main’: /<>/apbs/tools/mesh/tensor2dx.c:97:2: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c:98:2: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c:137:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c:138:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c:139:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c:140:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c:155:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c:156:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c:157:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/tensor2dx.c:158:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Linking C executable ../bin/mgmesh cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mgmesh.dir/link.txt --verbose=1 [ 59%] Linking C executable ../bin/uhbd_asc2bin /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mgmesh.dir/mgmesh.c.o -o ../bin/mgmesh ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -o ../bin/uhbd_asc2bin ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp [ 60%] Linking C executable ../bin/tensor2dx cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/tensor2dx.dir/tensor2dx.c.o -o ../bin/tensor2dx ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 60%] Built target mgmesh make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mergedx.dir/DependInfo.cmake --color= Scanning dependencies of target mergedx make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 61%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/mergedx.dir/mergedx.c.o -c /<>/apbs/tools/mesh/mergedx.c [ 61%] Built target uhbd_asc2bin make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/del2dx.dir/DependInfo.cmake --color= [ 61%] Built target tensor2dx make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake --color= Scanning dependencies of target del2dx make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' Scanning dependencies of target smooth make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build [ 62%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/del2dx.dir/del2dx.c.o -c /<>/apbs/tools/mesh/del2dx.c make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 63%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/smooth.dir/smooth.c.o -c /<>/apbs/tools/mesh/smooth.c /<>/apbs/tools/mesh/del2dx.c: In function ‘main’: /<>/apbs/tools/mesh/del2dx.c:76:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/del2dx.c:89:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/del2dx.c:97:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/del2dx.c:103:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/tools/mesh/del2dx.c:106:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Linking C executable ../bin/del2dx cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/del2dx.dir/del2dx.c.o -o ../bin/del2dx ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp [ 66%] Linking C executable ../bin/mergedx cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx.dir/mergedx.c.o -o ../bin/mergedx ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 66%] Built target mergedx make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake --color= [ 67%] Linking C executable ../bin/smooth cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/smooth.dir/link.txt --verbose=1 [ 67%] Built target del2dx make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mergedx2.dir/DependInfo.cmake --color= Scanning dependencies of target dxmath make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/smooth.dir/smooth.c.o -o ../bin/smooth ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' Scanning dependencies of target mergedx2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 68%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/dxmath.dir/dxmath.c.o -c /<>/apbs/tools/mesh/dxmath.c [ 69%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/mergedx2.dir/mergedx2.c.o -c /<>/apbs/tools/mesh/mergedx2.c /<>/apbs/src/routines.c: In function ‘writematMG’: /<>/apbs/src/routines.c:1840:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1840 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 69%] Built target smooth make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/benchmark.dir/DependInfo.cmake --color= Scanning dependencies of target benchmark make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 70%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/benchmark.dir/benchmark.c.o -c /<>/apbs/tools/mesh/benchmark.c /<>/apbs/src/routines.c: In function ‘writedataMG’: /<>/apbs/src/routines.c:2676:30: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2676 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2720:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2720 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2711:38: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2711 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2694:38: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2694 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2687:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2687 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2701:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2701 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2666:38: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2666 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 72%] Linking C executable ../bin/dxmath cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dxmath.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dxmath.dir/dxmath.c.o -o ../bin/dxmath ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp [ 73%] Linking C executable ../bin/benchmark cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/benchmark.dir/benchmark.c.o -o ../bin/benchmark ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 73%] Built target dxmath make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/depend make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dx2mol.dir/DependInfo.cmake --color= Scanning dependencies of target dx2mol [ 73%] Built target benchmark make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/depend make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/value.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' Scanning dependencies of target value make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/build [ 74%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/dx2mol.dir/dx2mol.c.o -c /<>/apbs/tools/mesh/dx2mol.c make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 75%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o [ 76%] Linking C executable ../bin/mergedx2 cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/value.dir/value.c.o -c /<>/apbs/tools/mesh/value.c /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx2.dir/mergedx2.c.o -o ../bin/mergedx2 ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp [ 77%] Linking C executable ../bin/value [ 79%] Linking C executable ../bin/dx2mol cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2mol.dir/link.txt --verbose=1 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/value.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2mol.dir/dx2mol.c.o -o ../bin/dx2mol ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/value.dir/value.c.o -o ../bin/value ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp [ 79%] Built target mergedx2 make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/multivalue.dir/DependInfo.cmake --color= Scanning dependencies of target multivalue make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 80%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/multivalue.dir/multivalue.c.o -c /<>/apbs/tools/mesh/multivalue.c make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 81%] Linking C shared library ../lib/libapbs_routines.so make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 [ 81%] Built target dx2mol make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/similarity.dir/DependInfo.cmake --color= /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so.3 -o ../lib/libapbs_routines.so.3 CMakeFiles/apbs_routines.dir/routines.c.o -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp ../lib/libapbs_mg.so.3 ../lib/libapbs_generic.so.3 ../lib/libapbs_pmgc.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp [ 81%] Built target value make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/analysis.dir/DependInfo.cmake --color= Scanning dependencies of target similarity make[4]: Leaving 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83%] Linking C executable ../bin/multivalue cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/multivalue.dir/link.txt --verbose=1 cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library ../lib/libapbs_routines.so.3 ../lib/libapbs_routines.so.3 ../lib/libapbs_routines.so [ 84%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/analysis.dir/analysis.c.o -c /<>/apbs/tools/mesh/analysis.c /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/multivalue.dir/multivalue.c.o -o ../bin/multivalue ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 84%] Built target apbs_routines make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/mesh /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/mesh /<>/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dx2uhbd.dir/DependInfo.cmake --color= Scanning dependencies of target dx2uhbd make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 86%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -c /<>/apbs/tools/mesh/dx2uhbd.c make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 86%] Built target multivalue make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/manip /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/manip /<>/obj-x86_64-linux-gnu/tools/manip/CMakeFiles/born.dir/DependInfo.cmake --color= Scanning dependencies of target born make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 87%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o cd /<>/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/born.dir/born.c.o -c /<>/apbs/tools/manip/born.c [ 88%] Linking C executable ../bin/similarity cd 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-Wl,--no-as-needed CMakeFiles/analysis.dir/analysis.c.o -o ../bin/analysis ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp [ 90%] Linking C executable ../bin/dx2uhbd cd /<>/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2uhbd.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp [ 91%] Linking C executable ../bin/born cd /<>/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/born.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/born.dir/born.c.o -o ../bin/born ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 91%] Built target analysis make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/manip /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/manip /<>/obj-x86_64-linux-gnu/tools/manip/CMakeFiles/coulomb.dir/DependInfo.cmake --color= Scanning dependencies of target coulomb make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 93%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o cd /<>/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/coulomb.dir/coulomb.c.o -c /<>/apbs/tools/manip/coulomb.c make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 93%] Built target similarity make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/tools/python /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/python /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/DependInfo.cmake --color= [ 93%] Built target born make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/apbs /<>/apbs/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src /<>/obj-x86_64-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake --color= Scanning dependencies of target _apbslib make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build Scanning dependencies of target apbs make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 93%] Built target dx2uhbd make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 94%] Building C object src/CMakeFiles/apbs.dir/main.c.o [ 95%] Linking C executable ../bin/coulomb cd /<>/obj-x86_64-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/coulomb.dir/link.txt --verbose=1 cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/apbs.dir/main.c.o -c /<>/apbs/src/main.c [ 96%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/coulomb.dir/coulomb.c.o -o ../bin/coulomb ../../lib/libapbs_mg.so.3 ../../lib/libapbs_pmgc.so.3 ../../lib/libapbs_generic.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cc -D_apbslib_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -I/usr/include/python3.8 -I/<>/apbs/tools/python -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fPIC -fopenmp -o CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /<>/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c [ 97%] Building C object src/CMakeFiles/apbs.dir/routines.c.o cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/<>/apbs/src -I/<>/obj-x86_64-linux-gnu/src -I/<>/apbs/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -fopenmp -o CMakeFiles/apbs.dir/routines.c.o -c /<>/apbs/src/routines.c /<>/apbs/src/main.c: In function ‘main’: /<>/apbs/src/main.c:288:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 288 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /<>/apbs/src/main.c:288:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 288 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 97%] Built target coulomb /<>/apbs/src/routines.c: In function ‘writematMG’: /<>/apbs/src/routines.c:1840:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1840 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c: In function ‘writedataMG’: /<>/apbs/src/routines.c:2676:30: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2676 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2720:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2720 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2711:38: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2711 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2694:38: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2694 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2687:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2687 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2701:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2701 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apbs/src/routines.c:2666:38: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2666 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/apbs/src/apbs.h:67, from /<>/apbs/src/routines.h:64, from /<>/apbs/src/routines.c:54: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Linking C executable ../bin/apbs cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -rdynamic CMakeFiles/apbs.dir/main.c.o CMakeFiles/apbs.dir/routines.c.o -o ../bin/apbs -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp ../lib/libapbs_routines.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp ../lib/libapbs_mg.so.3 ../lib/libapbs_generic.so.3 ../lib/libapbs_pmgc.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 98%] Built target apbs [100%] Linking C shared library ../../lib/_apbslib.so cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_apbslib.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,_apbslib.so -o ../../lib/_apbslib.so CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp ../../lib/libapbs_routines.so.3 /usr/lib/x86_64-linux-gnu/libpython3.8.so ../../lib/libapbs_mg.so.3 ../../lib/libapbs_generic.so.3 ../../lib/libapbs_pmgc.so.3 -lm -lstdc++ /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -lmaloc -fopenmp cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E copy /<>/obj-x86_64-linux-gnu/tools/python/apbslib.py /<>/apbs/../pdb2pqr/pdb2pka cd /<>/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E copy /<>/obj-x86_64-linux-gnu/lib/_apbslib.so /<>/apbs/../pdb2pqr/pdb2pka make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target _apbslib make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' (cd apbs/tests; PATH=/<>/obj-x86_64-linux-gnu/bin:${PATH} LD_LIBRARY_PATH=/<>/obj-x86_64-linux-gnu/lib:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/<>/apbs/tools/manip python3 apbs_tester.py -c test_cases.cfg; rm -rf __pycache__) Testing all sections The following sections will be tested: born, actin-dimer-auto, actin-dimer-parallel, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv, protein-rna ================================================================================ Running tests for born section -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.000988 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: apbs INPUT: apbs-mol-auto.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential-PE0.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-auto.out RESULT 960.7073836227 RESULT 2200.266567971 RESULT 4732.245131587 RESULT 1190.871482831 RESULT 2430.874049735 RESULT 4962.018684215 RESULT -229.7735526282 Testing computed result 9.607073836227E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 2.200266567971E+03 against expected result 2.200267E+03 *** PASSED *** Testing computed result 4.732245131587E+03 against expected result 4.732245E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.297735526282E+02 against expected result -2.297735E+02 *** PASSED *** Elapsed time: 9.737841 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: apbs INPUT: apbs-smol-auto.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-auto.out RESULT 953.292876745 RESULT 2201.243880085 RESULT 4733.006258977 RESULT 1190.871482831 RESULT 2430.874049735 RESULT 4962.018684215 RESULT -229.0124252387 Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 2.201243880085E+03 against expected result 2.201244E+03 *** PASSED *** Testing computed result 4.733006258977E+03 against expected result 4.733006E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.290124252387E+02 against expected result -2.290124E+02 *** PASSED *** Elapsed time: 7.768464 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: apbs INPUT: apbs-mol-parallel-PE0.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 2.401768459022E+02 8.142935592471E+02 1.485255308186E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.761864094552E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE1.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 2.401768459022E+02 8.142778312125E+02 1.485246667424E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.762728170718E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE2.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605696E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 2.401768459091E+02 8.142935605696E+02 1.485255306569E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.761864257239E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE3.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344954E+01 kJ/mol Global net ELEC energy = -5.762728344954E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 2.401768459091E+02 8.142778325440E+02 1.485246665692E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.762728344954E+01 RESULT 960.7073836226 RESULT 3257.1427835731997 RESULT 5941.0039478710005 RESULT 1190.8714828309999 RESULT 3519.7218230368003 RESULT 6171.495796544 RESULT -230.49184867463003 Testing computed result 9.607073836226E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 3.257142783573E+03 against expected result 3.257143E+03 *** PASSED *** Testing computed result 5.941003947871E+03 against expected result 5.941004E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.304918486746E+02 against expected result -2.304918E+02 *** PASSED *** Elapsed time: 42.247044 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: apbs INPUT: apbs-smol-parallel-PE0.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 2.383232191816E+02 8.145369591602E+02 1.485524998001E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734895113069E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE1.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 2.383232191816E+02 8.145419898332E+02 1.485529328612E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734462051928E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE2.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 2.383232191909E+02 8.145369593489E+02 1.485524997676E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734895146550E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE3.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 2.383232191909E+02 8.145419900310E+02 1.485529328301E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734462084052E+01 RESULT 953.292876745 RESULT 3258.1578983732998 RESULT 5942.108652589999 RESULT 1190.8714828309999 RESULT 3519.7218230368003 RESULT 6171.495796544 RESULT -229.38714395599 Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 3.258157898373E+03 against expected result 3.258158E+03 *** PASSED *** Testing computed result 5.942108652590E+03 against expected result 5.942109E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.293871439560E+02 against expected result -2.293871E+02 *** PASSED *** Elapsed time: 39.720586 seconds -------------------------------------------------------------------------------- Total elapsed time: 99.474923 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-auto section -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: apbs INPUT: apbs-mol-auto.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058625E+02 kJ/mol Global net ELEC energy = 1.048683058625E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-auto.out RESULT 152761.7850342 RESULT 291951.0754196 RESULT 152767.184488 RESULT 291546.8859278 RESULT 305631.7807611 RESULT 583602.8296532 RESULT 104.8683058625 Testing computed result 1.527617850342E+05 against expected result 1.527618E+05 *** PASSED *** Testing computed result 2.919510754196E+05 against expected result 2.919511E+05 *** PASSED *** Testing computed result 1.527671844880E+05 against expected result 1.527672E+05 *** PASSED *** Testing computed result 2.915468859278E+05 against expected result 2.915469E+05 *** PASSED *** Testing computed result 3.056317807611E+05 against expected result 3.056318E+05 *** PASSED *** Testing computed result 5.836028296532E+05 against expected result 5.836028E+05 *** PASSED *** Testing computed result 1.048683058625E+02 against expected result 1.048683E+02 *** PASSED *** Elapsed time: 130.902959 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: apbs INPUT: apbs-smol-auto.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077691E+02 kJ/mol Global net ELEC energy = 1.095841077691E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-auto.out RESULT 152863.2421825 RESULT 292061.866232 RESULT 152929.7900572 RESULT 291659.2202835 RESULT 305924.4262535 RESULT 583830.6706232 RESULT 109.5841077691 Testing computed result 1.528632421825E+05 against expected result 1.528632E+05 *** PASSED *** Testing computed result 2.920618662320E+05 against expected result 2.920619E+05 *** PASSED *** Testing computed result 1.529297900572E+05 against expected result 1.529298E+05 *** PASSED *** Testing computed result 2.916592202835E+05 against expected result 2.916592E+05 *** PASSED *** Testing computed result 3.059244262535E+05 against expected result 3.059244E+05 *** PASSED *** Testing computed result 5.838306706232E+05 against expected result 5.838307E+05 *** PASSED *** Testing computed result 1.095841077691E+02 against expected result 1.095841E+02 *** PASSED *** Elapsed time: 80.363082 seconds -------------------------------------------------------------------------------- Total elapsed time: 211.266041 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-parallel section -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 8 separate files using the inputgen utility BINARY: apbs INPUT: apbs-mol-parallel-PE0.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.335181353180E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.307364282738E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.892640552270E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.287357981689E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.237489755360E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595556713401E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.344489735005E+00 kJ/mol Global net ELEC energy = 8.344489735005E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 1.335181353180E+03 1.307364282738E+04 2.892640552270E+03 2.287357981689E+04 4.237489755360E+03 3.595556713401E+04 8.344489735005E+00 BINARY: apbs INPUT: apbs-mol-parallel-PE1.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161150884899E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.271349239954E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.084559511557E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.159185455930E-02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161009682231E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.271249973273E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -9.010749548674E-01 kJ/mol Global net ELEC energy = -9.010749548674E-01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 1.161150884899E+04 9.271349239954E+04 1.084559511557E-01 9.159185455930E-02 1.161009682231E+04 9.271249973273E+04 -9.010749548674E-01 BINARY: apbs INPUT: apbs-mol-parallel-PE2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.533327920982E+01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.349327483109E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.753646268927E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.716901575464E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.760706267384E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.753396861378E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.002011083293E+01 kJ/mol Global net ELEC energy = 3.002011083293E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 1.533327920982E+01 3.349327483109E+02 4.753646268927E+03 3.716901575464E+04 4.760706267384E+03 3.753396861378E+04 3.002011083293E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE3.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.803290534287E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.400275505449E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.150603559111E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.573366340513E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.804039178218E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.400354034488E+05 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.710240552123E+00 kJ/mol Global net ELEC energy = 8.710240552123E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 1.803290534287E+04 1.400275505449E+05 8.150603559111E-01 8.573366340513E-01 1.804039178218E+04 1.400354034488E+05 8.710240552123E+00 BINARY: apbs INPUT: apbs-mol-parallel-PE4.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.015087619451E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.216054441666E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.620207421716E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.273875050379E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.666622027749E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306246439444E+05 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.108446480104E+01 kJ/mol Global net ELEC energy = 2.108446480104E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE4.out Processor 4 results: 4.015087619451E+02 3.216054441666E+03 1.620207421716E+04 1.273875050379E+05 1.666622027749E+04 1.306246439444E+05 2.108446480104E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE5.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE5.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.100112513614E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.662571883858E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.370921758038E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.013366922344E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.115105077953E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.662768924081E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.371738924671E+00 kJ/mol Global net ELEC energy = 2.371738924671E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE5.out Processor 5 results: 2.100112513614E+03 1.662571883858E+04 4.370921758038E-01 4.013366922344E-01 2.115105077953E+03 1.662768924081E+04 2.371738924671E+00 BINARY: apbs INPUT: apbs-mol-parallel-PE6.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE6.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.817378781616E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.959534462269E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176793266728E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.643533578081E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176229449467E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.643148330287E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.892943480882E+00 kJ/mol Global net ELEC energy = -1.892943480882E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE6.out Processor 6 results: 2.817378781616E+00 1.959534462269E+00 1.176793266728E+04 9.643533578081E+04 1.176229449467E+04 9.643148330287E+04 -1.892943480882E+00 BINARY: apbs INPUT: apbs-mol-parallel-PE7.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-parallel-PE7.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.428230292158E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.199832997920E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.881300088062E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.152799174875E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.847712854852E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618156668929E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.043753521012E+01 kJ/mol Global net ELEC energy = 3.043753521012E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE7.out Processor 7 results: 2.428230292158E+03 2.199832997920E+04 3.881300088062E+02 4.152799174875E+03 2.847712854852E+03 2.618156668929E+04 3.043753521012E+01 RESULT 35927.59777074854 RESULT 287991.6813140391 RESULT 36005.78432292607 RESULT 288019.58583029587 RESULT 72040.017332199 RESULT 576102.8221066899 RESULT 98.17456162013961 Testing computed result 3.592759777075E+04 against expected result 3.592760E+04 *** PASSED *** Testing computed result 2.879916813140E+05 against expected result 2.879917E+05 *** PASSED *** Testing computed result 3.600578432293E+04 against expected result 3.600578E+04 *** PASSED *** Testing computed result 2.880195858303E+05 against expected result 2.880196E+05 *** PASSED *** Testing computed result 7.204001733220E+04 against expected result 7.204002E+04 *** PASSED *** Testing computed result 5.761028221067E+05 against expected result 5.761028E+05 *** PASSED *** Testing computed result 9.817456162014E+01 against expected result 9.817456E+01 *** PASSED *** Elapsed time: 562.296028 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 8 separate files using the inputgen utility BINARY: apbs INPUT: apbs-smol-parallel-PE0.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.371266245949E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.306912276054E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977036667733E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.288057348250E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.356039288708E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595842845220E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.732209150865E+00 kJ/mol Global net ELEC energy = 8.732209150865E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 1.371266245949E+03 1.306912276054E+04 2.977036667733E+03 2.288057348250E+04 4.356039288708E+03 3.595842845220E+04 8.732209150865E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE1.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183935033618E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.276168507128E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.420924995464E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.129046670919E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183791435221E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.276041697078E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.155195837104E+00 kJ/mol Global net ELEC energy = -1.155195837104E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 1.183935033618E+04 9.276168507128E+04 1.420924995464E-01 1.129046670919E-01 1.183791435221E+04 9.276041697078E+04 -1.155195837104E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.992726432058E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.375960934473E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.863608503641E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.720602537782E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.896854387650E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.757590620855E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.228473728523E+01 kJ/mol Global net ELEC energy = 3.228473728523E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 9.992726432058E+00 3.375960934473E+02 4.863608503641E+03 3.720602537782E+04 4.896854387650E+03 3.757590620855E+04 3.228473728523E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE3.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.826846317904E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.401007397614E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.966525690477E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.961424692860E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827933209233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.401092487740E+05 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 9.405155088028E+00 kJ/mol Global net ELEC energy = 9.405155088028E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 1.826846317904E+04 1.401007397614E+05 9.966525690477E-01 8.961424692860E-01 1.827933209233E+04 1.401092487740E+05 9.405155088028E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE4.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.021998204986E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.215581388579E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.644646339930E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.274227930024E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.689865332202E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306747503910E+05 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.637600005488E+01 kJ/mol Global net ELEC energy = 3.637600005488E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE4.out Processor 4 results: 4.021998204986E+02 3.215581388579E+03 1.644646339930E+04 1.274227930024E+05 1.689865332202E+04 1.306747503910E+05 3.637600005488E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE5.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE5.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.187673595319E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.663590032901E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.710032885061E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.849499127484E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189033693728E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.663641996916E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 1.004590063261E+00 kJ/mol Global net ELEC energy = 1.004590063261E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE5.out Processor 5 results: 2.187673595319E+03 1.663590032901E+04 4.710032885061E-01 4.849499127484E-01 2.189033693728E+03 1.663641996916E+04 1.004590063261E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE6.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE6.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.897659240526E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.552765434658E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.200266111088E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.646358551314E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.199560371894E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.645933328248E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.699465221478E+00 kJ/mol Global net ELEC energy = -1.699465221478E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE6.out Processor 6 results: 4.897659240526E+00 2.552765434658E+00 1.200266111088E+04 9.646358551314E+04 1.199560371894E+04 9.645933328248E+04 -1.699465221478E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE7.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-parallel-PE7.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.521894873214E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200161660501E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.033680106430E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.154432431334E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.960165191413E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618664307349E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.059403714563E+01 kJ/mol Global net ELEC energy = 3.059403714563E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE7.out Processor 7 results: 2.521894873214E+03 2.200161660501E+04 4.033680106430E+02 4.154432431334E+03 2.960165191413E+03 2.618664307349E+04 3.059403714563E+01 RESULT 36605.73843587318 RESULT 288124.794774701 RESULT 36694.74744055409 RESULT 288128.90380424313 RESULT 73413.59604699901 RESULT 576361.14712166 RESULT 115.54206772931201 Testing computed result 3.660573843587E+04 against expected result 3.660574E+04 *** PASSED *** Testing computed result 2.881247947747E+05 against expected result 2.881248E+05 *** PASSED *** Testing computed result 3.669474744055E+04 against expected result 3.669475E+04 *** PASSED *** Testing computed result 2.881289038042E+05 against expected result 2.881289E+05 *** PASSED *** Testing computed result 7.341359604700E+04 against expected result 7.341360E+04 *** PASSED *** Testing computed result 5.763611471217E+05 against expected result 5.763611E+05 *** PASSED *** Testing computed result 1.155420677293E+02 against expected result 1.155421E+02 *** PASSED *** Elapsed time: 364.453733 seconds -------------------------------------------------------------------------------- Total elapsed time: 926.749761 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for alkanes section -------------------------------------------------------------------------------- Testing input file alkanes.in BINARY: apbs INPUT: alkanes.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.267 MB high water Thanks for using APBS! Checking for intermidiate energies in input file alkanes.out RESULT 14.39739455792 RESULT 12.08346456826 RESULT 13.54016672221 RESULT 9.363673200142 RESULT 9.422717598546 RESULT 16.40068943201 RESULT 13.23144287435 RESULT 7.894367190329 RESULT 14.49633815052 RESULT 14.47900211546 RESULT 11.92358496286 Testing computed result 1.439739455792E+01 against expected result 1.439739E+01 *** PASSED *** Testing computed result 1.208346456826E+01 against expected result 1.208346E+01 *** PASSED *** Testing computed result 1.354016672221E+01 against expected result 1.354017E+01 *** PASSED *** Testing computed result 9.363673200142E+00 against expected result 9.363673E+00 *** PASSED *** Testing computed result 9.422717598546E+00 against expected result 9.422718E+00 *** PASSED *** Testing computed result 1.640068943201E+01 against expected result 1.640069E+01 *** PASSED *** Testing computed result 1.323144287435E+01 against expected result 1.323144E+01 *** PASSED *** Testing computed result 7.894367190329E+00 against expected result 7.894367E+00 *** PASSED *** Testing computed result 1.449633815052E+01 against expected result 1.449634E+01 *** PASSED *** Testing computed result 1.447900211546E+01 against expected result 1.447900E+01 *** PASSED *** Testing computed result 1.192358496286E+01 against expected result 1.192358E+01 *** PASSED *** Elapsed time: 9.600156 seconds -------------------------------------------------------------------------------- Total elapsed time: 9.600156 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for FKBP section -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in BINARY: apbs INPUT: 1d7h-dmso-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086371E+01 kJ/mol Global net ELEC energy = 1.500810086371E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7h-dmso-mol.out RESULT 10608.99690259 RESULT 42765.23673491 RESULT 13992.34956777 RESULT 46100.66575192 RESULT 39.61107503213 RESULT 712.1048606059 RESULT 67.51571424823 RESULT 733.9101343121 RESULT 10584.10584089 RESULT 42053.85249581 RESULT 13959.61902233 RESULT 45382.48433997 RESULT -3335.429017008 RESULT -21.80527370616 RESULT -3328.631844166 RESULT 15.00810086371 Testing computed result 1.060899690259E+04 against expected result 1.060900E+04 *** PASSED *** Testing computed result 4.276523673491E+04 against expected result 4.276524E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.961107503213E+01 against expected result 3.961108E+01 *** PASSED *** Testing computed result 7.121048606059E+02 against expected result 7.121049E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.058410584089E+04 against expected result 1.058411E+04 *** PASSED *** Testing computed result 4.205385249581E+04 against expected result 4.205385E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.500810086371E+01 against expected result 1.500810E+01 *** PASSED *** Elapsed time: 17.679154 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in BINARY: apbs INPUT: 1d7h-dmso-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192073E+01 kJ/mol Global net ELEC energy = 1.624454192073E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7h-dmso-smol.out RESULT 10749.48704824 RESULT 42894.87256481 RESULT 13992.34956777 RESULT 46100.66575192 RESULT 37.19709905887 RESULT 712.5747080979 RESULT 67.51571424823 RESULT 733.9101343121 RESULT 10716.54753674 RESULT 42181.78203716 RESULT 13959.61902233 RESULT 45382.48433997 RESULT -3205.793187109 RESULT -21.33542621421 RESULT -3200.702302816 RESULT 16.24454192073 Testing computed result 1.074948704824E+04 against expected result 1.074949E+04 *** PASSED *** Testing computed result 4.289487256481E+04 against expected result 4.289487E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.719709905887E+01 against expected result 3.719710E+01 *** PASSED *** Testing computed result 7.125747080979E+02 against expected result 7.125747E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.071654753674E+04 against expected result 1.071655E+04 *** PASSED *** Testing computed result 4.218178203716E+04 against expected result 4.218178E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.624454192073E+01 against expected result 1.624454E+01 *** PASSED *** Elapsed time: 15.834343 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in BINARY: apbs INPUT: 1d7i-dss-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933668E+01 kJ/mol Global net ELEC energy = 1.442499933668E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7i-dss-mol.out RESULT 9160.578033846 RESULT 39557.01871716 RESULT 12649.65939588 RESULT 43018.01664829 RESULT 94.31133325426 RESULT 1677.348113184 RESULT 117.1079106781 RESULT 1697.869784185 RESULT 9040.108332204 RESULT 37877.47796627 RESULT 12524.95566243 RESULT 41332.37922574 RESULT -3460.997931137 RESULT -20.52167100108 RESULT -3454.901259473 RESULT 14.42499933668 Testing computed result 9.160578033846E+03 against expected result 9.160578E+03 *** PASSED *** Testing computed result 3.955701871716E+04 against expected result 3.955702E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 9.431133325426E+01 against expected result 9.431133E+01 *** PASSED *** Testing computed result 1.677348113184E+03 against expected result 1.677348E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.040108332204E+03 against expected result 9.040108E+03 *** PASSED *** Testing computed result 3.787747796627E+04 against expected result 3.787748E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.442499933668E+01 against expected result 1.442501E+01 *** PASSED *** Elapsed time: 20.686031 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in BINARY: apbs INPUT: 1d7i-dss-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742844E+01 kJ/mol Global net ELEC energy = 1.545150742844E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7i-dss-smol.out RESULT 9634.884642408 RESULT 40031.77540425 RESULT 12649.65939588 RESULT 43018.01664829 RESULT 79.42232645345 RESULT 1677.798535473 RESULT 117.1079106781 RESULT 1697.869784185 RESULT 9507.068451372 RESULT 38350.75772299 RESULT 12524.95566243 RESULT 41332.37922574 RESULT -2986.24124404 RESULT -20.07124871262 RESULT -2981.621502756 RESULT 15.45150742844 Testing computed result 9.634884642408E+03 against expected result 9.634885E+03 *** PASSED *** Testing computed result 4.003177540425E+04 against expected result 4.003178E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 7.942232645345E+01 against expected result 7.942233E+01 *** PASSED *** Testing computed result 1.677798535473E+03 against expected result 1.677799E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.507068451372E+03 against expected result 9.507068E+03 *** PASSED *** Testing computed result 3.835075772299E+04 against expected result 3.835076E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.545150742844E+01 against expected result 1.545150E+01 *** PASSED *** Elapsed time: 15.933806 seconds -------------------------------------------------------------------------------- Total elapsed time: 70.133334 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for hca-bind section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: apbs INPUT: apbs-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812665E+01 kJ/mol Global net ELEC energy = -5.246475812665E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 221.3600726771 RESULT 1825.764811255 RESULT 6458.471211905 RESULT 20936.06095527 RESULT 151543.3544464 RESULT 178636.9323561 RESULT 21053.22784838 RESULT 153330.4996252 RESULT 185042.9388099 RESULT -52.46475812665 Testing computed result 2.213600726771E+02 against expected result 2.213601E+02 *** PASSED *** Testing computed result 1.825764811255E+03 against expected result 1.825765E+03 *** PASSED *** Testing computed result 6.458471211905E+03 against expected result 6.458471E+03 *** PASSED *** Testing computed result 2.093606095527E+04 against expected result 2.093606E+04 *** PASSED *** Testing computed result 1.515433544464E+05 against expected result 1.515434E+05 *** PASSED *** Testing computed result 1.786369323561E+05 against expected result 1.786369E+05 *** PASSED *** Testing computed result 2.105322784838E+04 against expected result 2.105323E+04 *** PASSED *** Testing computed result 1.533304996252E+05 against expected result 1.533305E+05 *** PASSED *** Testing computed result 1.850429388099E+05 against expected result 1.850429E+05 *** PASSED *** Testing computed result -5.246475812665E+01 against expected result -5.246476E+01 *** PASSED *** Elapsed time: 20.815836 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: apbs INPUT: apbs-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017066E+01 kJ/mol Global net ELEC energy = -5.405979017066E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 188.4888131017 RESULT 1820.045922544 RESULT 6460.002606908 RESULT 21891.61497021 RESULT 152000.0494925 RESULT 179043.619158 RESULT 21958.42512312 RESULT 153777.1604355 RESULT 185449.5619747 RESULT -54.05979017066 Testing computed result 1.884888131017E+02 against expected result 1.884888E+02 *** PASSED *** Testing computed result 1.820045922544E+03 against expected result 1.820046E+03 *** PASSED *** Testing computed result 6.460002606908E+03 against expected result 6.460003E+03 *** PASSED *** Testing computed result 2.189161497021E+04 against expected result 2.189161E+04 *** PASSED *** Testing computed result 1.520000494925E+05 against expected result 1.520000E+05 *** PASSED *** Testing computed result 1.790436191580E+05 against expected result 1.790436E+05 *** PASSED *** Testing computed result 2.195842512312E+04 against expected result 2.195843E+04 *** PASSED *** Testing computed result 1.537771604355E+05 against expected result 1.537772E+05 *** PASSED *** Testing computed result 1.854495619747E+05 against expected result 1.854496E+05 *** PASSED *** Testing computed result -5.405979017066E+01 against expected result -5.405978E+01 *** PASSED *** Elapsed time: 13.258749 seconds -------------------------------------------------------------------------------- Total elapsed time: 34.074585 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ionize section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: apbs INPUT: apbs-mol.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 5823.898055191 RESULT 9793.274462353 RESULT 5846.917564309 RESULT 9815.953282539 RESULT 8219.846763777 RESULT 13927.41988698 RESULT 8420.373979905 RESULT 14127.16615065 RESULT 3862.359524598 RESULT 6288.15625161 RESULT 4162.533113906 RESULT 6585.616091973 RESULT -22.67882018629 RESULT -199.7462636633 RESULT -297.4598403628 RESULT -474.5272838398 Testing computed result 5.823898055191E+03 against expected result 5.823898E+03 *** PASSED *** Testing computed result 9.793274462353E+03 against expected result 9.793274E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.219846763777E+03 against expected result 8.219847E+03 *** PASSED *** Testing computed result 1.392741988698E+04 against expected result 1.392742E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.862359524598E+03 against expected result 3.862360E+03 *** PASSED *** Testing computed result 6.288156251610E+03 against expected result 6.288156E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.267882018629E+01 against expected result -2.267882E+01 *** PASSED *** Testing computed result -1.997462636633E+02 against expected result -1.997463E+02 *** PASSED *** Testing computed result -2.974598403628E+02 against expected result -2.974598E+02 *** PASSED *** Testing computed result -4.745272838398E+02 against expected result -4.745273E+02 *** PASSED *** Elapsed time: 13.350298 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: apbs INPUT: apbs-smol.in ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 5824.172730822 RESULT 9793.622759239 RESULT 5846.917564309 RESULT 9815.953282539 RESULT 8221.328580569 RESULT 13928.67783119 RESULT 8420.373979905 RESULT 14127.16615065 RESULT 3863.066835285 RESULT 6289.649216644 RESULT 4162.533113906 RESULT 6585.616091973 RESULT -22.33052329981 RESULT -198.4883194538 RESULT -295.9668753288 RESULT -472.1246714828 Testing computed result 5.824172730822E+03 against expected result 5.824173E+03 *** PASSED *** Testing computed result 9.793622759239E+03 against expected result 9.793623E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.221328580569E+03 against expected result 8.221329E+03 *** PASSED *** Testing computed result 1.392867783119E+04 against expected result 1.392868E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.863066835285E+03 against expected result 3.863067E+03 *** PASSED *** Testing computed result 6.289649216644E+03 against expected result 6.289649E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.233052329981E+01 against expected result -2.233050E+01 *** PASSED *** Testing computed result -1.984883194538E+02 against expected result -1.984883E+02 *** PASSED *** Testing computed result -2.959668753288E+02 against expected result -2.959669E+02 *** PASSED *** Testing computed result -4.721246714828E+02 against expected result -4.721247E+02 *** PASSED *** Elapsed time: 11.294319 seconds -------------------------------------------------------------------------------- Total elapsed time: 24.644617 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-pmf section -------------------------------------------------------------------------------- Testing input file ion-pmf.in BINARY: apbs INPUT: ion-pmf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.106 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.155 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.130e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.767e-05 tot 1 -2.723e-02 9.133e-07 9.133e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.767e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718359932E+00 WCA energy for atom 1: -6.909422551724E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365308087297E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365308087297E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.250 MB high water Thanks for using APBS! Checking for intermidiate energies in input file ion-pmf.out RESULT 7839.535983197 RESULT 8964.727588811 RESULT -1125.191605614 RESULT -13.65308087297 Testing computed result 7.839535983197E+03 against expected result 7.839536E+03 *** PASSED *** Testing computed result 8.964727588811E+03 against expected result 8.964728E+03 *** PASSED *** Testing computed result -1.125191605614E+03 against expected result -1.125192E+03 *** PASSED *** Elapsed time: 7.217692 seconds -------------------------------------------------------------------------------- Total elapsed time: 7.217692 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for pka-lig section -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in BINARY: apbs INPUT: apbs-mol-vdw.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648730E+00 kJ/mol Global net ELEC energy = 8.083515648730E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-vdw.out RESULT 2224.988750664 RESULT 10496.95084686 RESULT 181845.0789522 RESULT 300825.4338259 RESULT 184091.8409896 RESULT 311330.4681884 RESULT 8.08351564873 Testing computed result 2.224988750664E+03 against expected result 2.224989E+03 *** PASSED *** Testing computed result 1.049695084686E+04 against expected result 1.049695E+04 *** PASSED *** Testing computed result 1.818450789522E+05 against expected result 1.818451E+05 *** PASSED *** Testing computed result 3.008254338259E+05 against expected result 3.008254E+05 *** PASSED *** Testing computed result 1.840918409896E+05 against expected result 1.840918E+05 *** PASSED *** Testing computed result 3.113304681884E+05 against expected result 3.113305E+05 *** PASSED *** Testing computed result 8.083515648730E+00 against expected result 8.083516E+00 *** PASSED *** Elapsed time: 17.756951 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in BINARY: apbs INPUT: apbs-smol-vdw.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255723E+01 kJ/mol Global net ELEC energy = 2.096300255723E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-vdw.out RESULT 2226.793167046 RESULT 10505.04485887 RESULT 182797.6621645 RESULT 301722.8546773 RESULT 185081.9075387 RESULT 312248.8625388 RESULT 20.96300255723 Testing computed result 2.226793167046E+03 against expected result 2.226793E+03 *** PASSED *** Testing computed result 1.050504485887E+04 against expected result 1.050504E+04 *** PASSED *** Testing computed result 1.827976621645E+05 against expected result 1.827977E+05 *** PASSED *** Testing computed result 3.017228546773E+05 against expected result 3.017229E+05 *** PASSED *** Testing computed result 1.850819075387E+05 against expected result 1.850819E+05 *** PASSED *** Testing computed result 3.122488625388E+05 against expected result 3.122489E+05 *** PASSED *** Testing computed result 2.096300255723E+01 against expected result 2.096296E+01 *** PASSED *** Elapsed time: 13.323768 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in BINARY: apbs INPUT: apbs-mol-surf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686581E+02 kJ/mol Global net ELEC energy = 1.192607686581E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-surf.out RESULT 2244.350164274 RESULT 10521.49475373 RESULT 186261.5690066 RESULT 305181.0884053 RESULT 188662.5455219 RESULT 315821.8439277 RESULT 119.2607686581 Testing computed result 2.244350164274E+03 against expected result 2.244350E+03 *** PASSED *** Testing computed result 1.052149475373E+04 against expected result 1.052149E+04 *** PASSED *** Testing computed result 1.862615690066E+05 against expected result 1.862616E+05 *** PASSED *** Testing computed result 3.051810884053E+05 against expected result 3.051811E+05 *** PASSED *** Testing computed result 1.886625455219E+05 against expected result 1.886625E+05 *** PASSED *** Testing computed result 3.158218439277E+05 against expected result 3.158218E+05 *** PASSED *** Testing computed result 1.192607686581E+02 against expected result 1.192608E+02 *** PASSED *** Elapsed time: 15.797324 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in BINARY: apbs INPUT: apbs-smol-surf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-surf.out RESULT 2251.46678942 RESULT 10528.14502873 RESULT 186407.1689626 RESULT 305331.9953673 RESULT 188802.7142979 RESULT 315969.0177241 RESULT 108.8773280806 Testing computed result 2.251466789420E+03 against expected result 2.251467E+03 *** PASSED *** Testing computed result 1.052814502873E+04 against expected result 1.052815E+04 *** PASSED *** Testing computed result 1.864071689626E+05 against expected result 1.864072E+05 *** PASSED *** Testing computed result 3.053319953673E+05 against expected result 3.053320E+05 *** PASSED *** Testing computed result 1.888027142979E+05 against expected result 1.888027E+05 *** PASSED *** Testing computed result 3.159690177241E+05 against expected result 3.159690E+05 *** PASSED *** Testing computed result 1.088773280806E+02 against expected result 1.088773E+02 *** PASSED *** Elapsed time: 13.243968 seconds -------------------------------------------------------------------------------- Total elapsed time: 60.122011 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for point-pmf section -------------------------------------------------------------------------------- Testing input file complex-0_1.in BINARY: apbs INPUT: complex-0_1.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.067 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_1.out RESULT 97.76035707281 RESULT 89.75920687031 RESULT 205.8277719334 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 89.7592 RESULT 205.828 RESULT 96.5336 RESULT 88.6151 RESULT 201.106 RESULT 18.30820799027 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 8.975920687031E+01 against expected result 8.975921E+01 *** PASSED *** Testing computed result 2.058277719334E+02 against expected result 2.058278E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 8.975920000000E+01 against expected result 8.975920E+01 *** PASSED *** Testing computed result 2.058280000000E+02 against expected result 2.058280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 8.861510000000E+01 against expected result 8.861510E+01 *** PASSED *** Testing computed result 2.011060000000E+02 against expected result 2.011060E+02 *** PASSED *** Testing computed result 1.830820799027E+01 against expected result 1.830821E+01 *** PASSED *** Elapsed time: 3.411697 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in BINARY: apbs INPUT: complex-0_2.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086750E+00 kJ/mol Global net ELEC energy = 8.906694086750E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_2.out RESULT 97.76035707281 RESULT 101.7611498797 RESULT 208.4282010393 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 101.761 RESULT 208.428 RESULT 96.5336 RESULT 100.656 RESULT 203.83 RESULT 8.90669408675 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.084282010393E+02 against expected result 2.084282E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.084280000000E+02 against expected result 2.084280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006560000000E+02 against expected result 1.006560E+02 *** PASSED *** Testing computed result 2.038300000000E+02 against expected result 2.038300E+02 *** PASSED *** Testing computed result 8.906694086750E+00 against expected result 8.906694E+00 *** PASSED *** Elapsed time: 3.030878 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in BINARY: apbs INPUT: complex-0_3.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_3.out RESULT 97.76035707281 RESULT 133.7661883222 RESULT 237.436145212 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 133.766 RESULT 237.436 RESULT 96.5336 RESULT 132.672 RESULT 232.924 RESULT 5.909599816984 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.337661883222E+02 against expected result 1.337662E+02 *** PASSED *** Testing computed result 2.374361452120E+02 against expected result 2.374361E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.337660000000E+02 against expected result 1.337660E+02 *** PASSED *** Testing computed result 2.374360000000E+02 against expected result 2.374360E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.326720000000E+02 against expected result 1.326720E+02 *** PASSED *** Testing computed result 2.329240000000E+02 against expected result 2.329240E+02 *** PASSED *** Testing computed result 5.909599816984E+00 against expected result 5.909600E+00 *** PASSED *** Elapsed time: 3.249738 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in BINARY: apbs INPUT: complex-0_4.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.061 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_4.out RESULT 97.76035707281 RESULT 101.7611498797 RESULT 203.9516519 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 101.761 RESULT 203.952 RESULT 96.5336 RESULT 100.654 RESULT 199.493 RESULT 4.430144947418 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.039516519000E+02 against expected result 2.039517E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.039520000000E+02 against expected result 2.039520E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006540000000E+02 against expected result 1.006540E+02 *** PASSED *** Testing computed result 1.994930000000E+02 against expected result 1.994930E+02 *** PASSED *** Testing computed result 4.430144947418E+00 against expected result 4.430145E+00 *** PASSED *** Elapsed time: 2.291060 seconds -------------------------------------------------------------------------------- Total elapsed time: 11.983373 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for solv section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: apbs INPUT: apbs-mol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488074E+01 kJ/mol Global net ELEC energy = -3.624863488074E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 1847.663548071 RESULT 1883.912182952 RESULT 2732.623683321 RESULT 3123.035854133 RESULT -36.24863488074 RESULT -390.4121708125 RESULT -354.1635359318 Testing computed result 1.847663548071E+03 against expected result 1.847664E+03 *** PASSED *** Testing computed result 1.883912182952E+03 against expected result 1.883912E+03 *** PASSED *** Testing computed result 2.732623683321E+03 against expected result 2.732624E+03 *** PASSED *** Testing computed result 3.123035854133E+03 against expected result 3.123036E+03 *** PASSED *** Testing computed result -3.624863488074E+01 against expected result -3.624863E+01 *** PASSED *** Testing computed result -3.904121708125E+02 against expected result -3.904121E+02 *** PASSED *** Testing computed result -3.541635359318E+02 against expected result -3.541635E+02 *** PASSED *** Elapsed time: 4.205560 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: apbs INPUT: apbs-smol.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772493E+01 kJ/mol Global net ELEC energy = -3.757593772493E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Creating file now: apbs-0.025.in Creating file now: apbs-0.050.in Creating file now: apbs-0.075.in Creating file now: apbs-0.100.in Creating file now: apbs-0.125.in Creating file now: apbs-0.150.in Creating file now: apbs-0.175.in Creating file now: apbs-0.200.in Creating file now: apbs-0.225.in Creating file now: apbs-0.250.in Creating file now: apbs-0.275.in Creating file now: apbs-0.300.in Creating file now: apbs-0.325.in Creating file now: apbs-0.400.in Creating file now: apbs-0.500.in Creating file now: apbs-0.600.in Creating file now: apbs-0.700.in Creating file now: apbs-0.800.in Creating file_2 now: dxmath-0.025.in Creating file_2 now: dxmath-0.050.in Creating file_2 now: dxmath-0.075.in Creating file_2 now: dxmath-0.100.in Creating file_2 now: dxmath-0.125.in Creating file_2 now: dxmath-0.150.in Creating file_2 now: dxmath-0.175.in Creating file_2 now: dxmath-0.200.in Creating file_2 now: dxmath-0.225.in Creating file_2 now: dxmath-0.250.in Creating file_2 now: dxmath-0.275.in Creating file_2 now: dxmath-0.300.in Creating file_2 now: dxmath-0.325.in Creating file_2 now: dxmath-0.400.in Creating file_2 now: dxmath-0.500.in Creating file_2 now: dxmath-0.600.in Creating file_2 now: dxmath-0.700.in Creating file_2 now: dxmath-0.800.in Checking for intermidiate energies in input file apbs-smol.out RESULT 1847.86044002 RESULT 1885.436377745 RESULT 2734.040568569 RESULT 3125.279428954 RESULT -37.57593772493 RESULT -391.2388603848 RESULT -353.6629226599 Testing computed result 1.847860440020E+03 against expected result 1.847860E+03 *** PASSED *** Testing computed result 1.885436377745E+03 against expected result 1.885436E+03 *** PASSED *** Testing computed result 2.734040568569E+03 against expected result 2.734041E+03 *** PASSED *** Testing computed result 3.125279428954E+03 against expected result 3.125279E+03 *** PASSED *** Testing computed result -3.757593772493E+01 against expected result -3.757594E+01 *** PASSED *** Testing computed result -3.912388603848E+02 against expected result -3.912388E+02 *** PASSED *** Testing computed result -3.536629226599E+02 against expected result -3.536629E+02 *** PASSED *** Elapsed time: 4.279202 seconds -------------------------------------------------------------------------------- Total elapsed time: 8.484762 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for protein-rna section -------------------------------------------------------------------------------- Testing input file apbs-0.025.in BINARY: apbs INPUT: apbs-0.025.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.025.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.186122223752E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.025.dx Ion number density to be written to ndens-complex-0.025.dx Total electrostatic energy = 3.662855899462E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.025-PE0.dx Writing number density to ndens-complex-0.025-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.477786964834E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.025.dx Ion number density to be written to ndens-pep-0.025.dx Total electrostatic energy = 1.000545153104E+04 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.025-PE0.dx Writing number density to ndens-pep-0.025-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.329205982055E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 19.4227 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.025 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.025 M concentration 2.000 A-radius, -1.000 e-charge, 0.025 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.025.dx Ion number density to be written to ndens-rna-0.025.dx Total electrostatic energy = 2.653636629928E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.025-PE0.dx Writing number density to ndens-rna-0.025-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 8.674116429351E+01 kJ/mol Global net ELEC energy = 8.674116429351E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31861.22223752 RESULT 36628.55899462 RESULT 8477.786964834 RESULT 10005.45153104 RESULT 23292.05982055 RESULT 26536.36629928 RESULT 86.74116429351 Testing computed result 3.186122223752E+04 against expected result 3.186122E+04 *** PASSED *** Testing computed result 3.662855899462E+04 against expected result 3.662856E+04 *** PASSED *** Testing computed result 8.477786964834E+03 against expected result 8.477787E+03 *** PASSED *** Testing computed result 1.000545153104E+04 against expected result 1.000545E+04 *** PASSED *** Testing computed result 2.329205982055E+04 against expected result 2.329206E+04 *** PASSED *** Testing computed result 2.653636629928E+04 against expected result 2.653637E+04 *** PASSED *** Testing computed result 8.674116429351E+01 against expected result 8.674116E+01 *** PASSED *** Elapsed time: 47.950425 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.050.in BINARY: apbs INPUT: apbs-0.050.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.050.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.184763478312E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.050.dx Ion number density to be written to ndens-complex-0.050.dx Total electrostatic energy = 3.661493366846E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.050-PE0.dx Writing number density to ndens-complex-0.050-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.475252516617E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.050.dx Ion number density to be written to ndens-pep-0.050.dx Total electrostatic energy = 1.000292179294E+04 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.050-PE0.dx Writing number density to ndens-pep-0.050-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.327168361816E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.7339 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.050.dx Ion number density to be written to ndens-rna-0.050.dx Total electrostatic energy = 2.651594350839E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.050-PE0.dx Writing number density to ndens-rna-0.050-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 9.606836713868E+01 kJ/mol Global net ELEC energy = 9.606836713868E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31847.63478312 RESULT 36614.93366846 RESULT 8475.252516617 RESULT 10002.92179294 RESULT 23271.68361816 RESULT 26515.94350839 RESULT 96.06836713868 Testing computed result 3.184763478312E+04 against expected result 3.184763E+04 *** PASSED *** Testing computed result 3.661493366846E+04 against expected result 3.661493E+04 *** PASSED *** Testing computed result 8.475252516617E+03 against expected result 8.475253E+03 *** PASSED *** Testing computed result 1.000292179294E+04 against expected result 1.000292E+04 *** PASSED *** Testing computed result 2.327168361816E+04 against expected result 2.327168E+04 *** PASSED *** Testing computed result 2.651594350839E+04 against expected result 2.651594E+04 *** PASSED *** Testing computed result 9.606836713868E+01 against expected result 9.606837E+01 *** PASSED *** Elapsed time: 48.572585 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.075.in BINARY: apbs INPUT: apbs-0.075.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.075.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.184033569905E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.075.dx Ion number density to be written to ndens-complex-0.075.dx Total electrostatic energy = 3.660761530545E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.075-PE0.dx Writing number density to ndens-complex-0.075-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.473669396547E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.075.dx Ion number density to be written to ndens-pep-0.075.dx Total electrostatic energy = 1.000134276339E+04 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.075-PE0.dx Writing number density to ndens-pep-0.075-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.326088212207E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 11.2137 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.075 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.075 M concentration 2.000 A-radius, -1.000 e-charge, 0.075 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.075.dx Ion number density to be written to ndens-rna-0.075.dx Total electrostatic energy = 2.650511882057E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.075-PE0.dx Writing number density to ndens-rna-0.075-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.011537214883E+02 kJ/mol Global net ELEC energy = 1.011537214883E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31840.33569905 RESULT 36607.61530545 RESULT 8473.669396547 RESULT 10001.34276339 RESULT 23260.88212207 RESULT 26505.11882057 RESULT 101.1537214883 Testing computed result 3.184033569905E+04 against expected result 3.184034E+04 *** PASSED *** Testing computed result 3.660761530545E+04 against expected result 3.660762E+04 *** PASSED *** Testing computed result 8.473669396547E+03 against expected result 8.473669E+03 *** PASSED *** Testing computed result 1.000134276339E+04 against expected result 1.000134E+04 *** PASSED *** Testing computed result 2.326088212207E+04 against expected result 2.326088E+04 *** PASSED *** Testing computed result 2.650511882057E+04 against expected result 2.650512E+04 *** PASSED *** Testing computed result 1.011537214883E+02 against expected result 1.011537E+02 *** PASSED *** Elapsed time: 41.555933 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.100.in BINARY: apbs INPUT: apbs-0.100.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.100.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.183548000794E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.100.dx Ion number density to be written to ndens-complex-0.100.dx Total electrostatic energy = 3.660274809589E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.100-PE0.dx Writing number density to ndens-complex-0.100-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.472507235893E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.100.dx Ion number density to be written to ndens-pep-0.100.dx Total electrostatic energy = 1.000018407412E+04 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.100-PE0.dx Writing number density to ndens-pep-0.100-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.325372656922E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 9.71135 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.100 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.100 M concentration 2.000 A-radius, -1.000 e-charge, 0.100 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.100.dx Ion number density to be written to ndens-rna-0.100.dx Total electrostatic energy = 2.649794981016E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.100-PE0.dx Writing number density to ndens-rna-0.100-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.046142116108E+02 kJ/mol Global net ELEC energy = 1.046142116108E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31835.48000794 RESULT 36602.74809589 RESULT 8472.507235893 RESULT 10000.18407412 RESULT 23253.72656922 RESULT 26497.94981016 RESULT 104.6142116108 Testing computed result 3.183548000794E+04 against expected result 3.183548E+04 *** PASSED *** Testing computed result 3.660274809589E+04 against expected result 3.660275E+04 *** PASSED *** Testing computed result 8.472507235893E+03 against expected result 8.472507E+03 *** PASSED *** Testing computed result 1.000018407412E+04 against expected result 1.000018E+04 *** PASSED *** Testing computed result 2.325372656922E+04 against expected result 2.325373E+04 *** PASSED *** Testing computed result 2.649794981016E+04 against expected result 2.649795E+04 *** PASSED *** Testing computed result 1.046142116108E+02 against expected result 1.046142E+02 *** PASSED *** Elapsed time: 49.512656 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.125.in BINARY: apbs INPUT: apbs-0.125.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.125.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.183190100647E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.125.dx Ion number density to be written to ndens-complex-0.125.dx Total electrostatic energy = 3.659916161996E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.125-PE0.dx Writing number density to ndens-complex-0.125-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.471585837513E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.125.dx Ion number density to be written to ndens-pep-0.125.dx Total electrostatic energy = 9.999265654586E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.125-PE0.dx Writing number density to ndens-pep-0.125-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.324845847155E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 8.6861 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.125 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.125 M concentration 2.000 A-radius, -1.000 e-charge, 0.125 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.125.dx Ion number density to be written to ndens-rna-0.125.dx Total electrostatic energy = 2.649267328362E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.125-PE0.dx Writing number density to ndens-rna-0.125-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.072226817610E+02 kJ/mol Global net ELEC energy = 1.072226817610E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31831.90100647 RESULT 36599.16161996 RESULT 8471.585837513 RESULT 9999.265654586 RESULT 23248.45847155 RESULT 26492.67328362 RESULT 107.222681761 Testing computed result 3.183190100647E+04 against expected result 3.183190E+04 *** PASSED *** Testing computed result 3.659916161996E+04 against expected result 3.659916E+04 *** PASSED *** Testing computed result 8.471585837513E+03 against expected result 8.471586E+03 *** PASSED *** Testing computed result 9.999265654586E+03 against expected result 9.999266E+03 *** PASSED *** Testing computed result 2.324845847155E+04 against expected result 2.324846E+04 *** PASSED *** Testing computed result 2.649267328362E+04 against expected result 2.649267E+04 *** PASSED *** Testing computed result 1.072226817610E+02 against expected result 1.072227E+02 *** PASSED *** Elapsed time: 53.015056 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.150.in BINARY: apbs INPUT: apbs-0.150.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.150.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182909678356E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.150.dx Ion number density to be written to ndens-complex-0.150.dx Total electrostatic energy = 3.659635228953E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.150-PE0.dx Writing number density to ndens-complex-0.150-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.470821300868E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.150.dx Ion number density to be written to ndens-pep-0.150.dx Total electrostatic energy = 9.998503715551E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.150-PE0.dx Writing number density to ndens-pep-0.150-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.324433086171E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.92928 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.150.dx Ion number density to be written to ndens-rna-0.150.dx Total electrostatic energy = 2.648854016160E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.150-PE0.dx Writing number density to ndens-rna-0.150-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.093084123761E+02 kJ/mol Global net ELEC energy = 1.093084123761E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31829.09678356 RESULT 36596.35228953 RESULT 8470.821300868 RESULT 9998.503715551 RESULT 23244.33086171 RESULT 26488.5401616 RESULT 109.3084123761 Testing computed result 3.182909678356E+04 against expected result 3.182910E+04 *** PASSED *** Testing computed result 3.659635228953E+04 against expected result 3.659635E+04 *** PASSED *** Testing computed result 8.470821300868E+03 against expected result 8.470821E+03 *** PASSED *** Testing computed result 9.998503715551E+03 against expected result 9.998504E+03 *** PASSED *** Testing computed result 2.324433086171E+04 against expected result 2.324433E+04 *** PASSED *** Testing computed result 2.648854016160E+04 against expected result 2.648854E+04 *** PASSED *** Testing computed result 1.093084123761E+02 against expected result 1.093084E+02 *** PASSED *** Elapsed time: 54.956795 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.175.in BINARY: apbs INPUT: apbs-0.175.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.175.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182680817429E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.175.dx Ion number density to be written to ndens-complex-0.175.dx Total electrostatic energy = 3.659406006570E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.175-PE0.dx Writing number density to ndens-complex-0.175-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.470167484600E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.175.dx Ion number density to be written to ndens-pep-0.175.dx Total electrostatic energy = 9.997852199372E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.175-PE0.dx Writing number density to ndens-pep-0.175-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.324096101131E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.34109 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.175 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.175 M concentration 2.000 A-radius, -1.000 e-charge, 0.175 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.175.dx Ion number density to be written to ndens-rna-0.175.dx Total electrostatic energy = 2.648516662194E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.175-PE0.dx Writing number density to ndens-rna-0.175-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.110412443878E+02 kJ/mol Global net ELEC energy = 1.110412443878E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31826.80817429 RESULT 36594.0600657 RESULT 8470.1674846 RESULT 9997.852199372 RESULT 23240.96101131 RESULT 26485.16662194 RESULT 111.0412443878 Testing computed result 3.182680817429E+04 against expected result 3.182681E+04 *** PASSED *** Testing computed result 3.659406006570E+04 against expected result 3.659406E+04 *** PASSED *** Testing computed result 8.470167484600E+03 against expected result 8.470167E+03 *** PASSED *** Testing computed result 9.997852199372E+03 against expected result 9.997852E+03 *** PASSED *** Testing computed result 2.324096101131E+04 against expected result 2.324096E+04 *** PASSED *** Testing computed result 2.648516662194E+04 against expected result 2.648517E+04 *** PASSED *** Testing computed result 1.110412443878E+02 against expected result 1.110412E+02 *** PASSED *** Elapsed time: 54.962676 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.200.in BINARY: apbs INPUT: apbs-0.200.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.200.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182488501939E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.200.dx Ion number density to be written to ndens-complex-0.200.dx Total electrostatic energy = 3.659213428941E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.200-PE0.dx Writing number density to ndens-complex-0.200-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.469596195763E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.200.dx Ion number density to be written to ndens-pep-0.200.dx Total electrostatic energy = 9.997282974485E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.200-PE0.dx Writing number density to ndens-pep-0.200-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.323812822097E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.86696 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.200 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.200 M concentration 2.000 A-radius, -1.000 e-charge, 0.200 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.200.dx Ion number density to be written to ndens-rna-0.200.dx Total electrostatic energy = 2.648233134327E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.200-PE0.dx Writing number density to ndens-rna-0.200-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.125199716537E+02 kJ/mol Global net ELEC energy = 1.125199716537E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31824.88501939 RESULT 36592.13428941 RESULT 8469.596195763 RESULT 9997.282974485 RESULT 23238.12822097 RESULT 26482.33134327 RESULT 112.5199716537 Testing computed result 3.182488501939E+04 against expected result 3.182489E+04 *** PASSED *** Testing computed result 3.659213428941E+04 against expected result 3.659213E+04 *** PASSED *** Testing computed result 8.469596195763E+03 against expected result 8.469596E+03 *** PASSED *** Testing computed result 9.997282974485E+03 against expected result 9.997283E+03 *** PASSED *** Testing computed result 2.323812822097E+04 against expected result 2.323813E+04 *** PASSED *** Testing computed result 2.648233134327E+04 against expected result 2.648233E+04 *** PASSED *** Testing computed result 1.125199716537E+02 against expected result 1.125200E+02 *** PASSED *** Elapsed time: 53.727204 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.225.in BINARY: apbs INPUT: apbs-0.225.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.225.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182323306491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.225.dx Ion number density to be written to ndens-complex-0.225.dx Total electrostatic energy = 3.659048040133E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.225-PE0.dx Writing number density to ndens-complex-0.225-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.469088900775E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.225.dx Ion number density to be written to ndens-pep-0.225.dx Total electrostatic energy = 9.996777552566E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.225-PE0.dx Writing number density to ndens-pep-0.225-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.323569434544E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.47423 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.225 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.225 M concentration 2.000 A-radius, -1.000 e-charge, 0.225 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.225.dx Ion number density to be written to ndens-rna-0.225.dx Total electrostatic energy = 2.647989580221E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.225-PE0.dx Writing number density to ndens-rna-0.225-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.138070465620E+02 kJ/mol Global net ELEC energy = 1.138070465620E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31823.23306491 RESULT 36590.48040133 RESULT 8469.088900775 RESULT 9996.777552566 RESULT 23235.69434544 RESULT 26479.89580221 RESULT 113.807046562 Testing computed result 3.182323306491E+04 against expected result 3.182323E+04 *** PASSED *** Testing computed result 3.659048040133E+04 against expected result 3.659048E+04 *** PASSED *** Testing computed result 8.469088900775E+03 against expected result 8.469089E+03 *** PASSED *** Testing computed result 9.996777552566E+03 against expected result 9.996778E+03 *** PASSED *** Testing computed result 2.323569434544E+04 against expected result 2.323569E+04 *** PASSED *** Testing computed result 2.647989580221E+04 against expected result 2.647990E+04 *** PASSED *** Testing computed result 1.138070465620E+02 against expected result 1.138070E+02 *** PASSED *** Elapsed time: 55.586248 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.250.in BINARY: apbs INPUT: apbs-0.250.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.250.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182178954360E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.250.dx Ion number density to be written to ndens-complex-0.250.dx Total electrostatic energy = 3.658903543806E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.250-PE0.dx Writing number density to ndens-complex-0.250-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.468632740499E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.250.dx Ion number density to be written to ndens-pep-0.250.dx Total electrostatic energy = 9.996323108319E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.250-PE0.dx Writing number density to ndens-pep-0.250-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.323356752071E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 6.142 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.250 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.250 M concentration 2.000 A-radius, -1.000 e-charge, 0.250 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.250.dx Ion number density to be written to ndens-rna-0.250.dx Total electrostatic energy = 2.647776789284E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.250-PE0.dx Writing number density to ndens-rna-0.250-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.149444369079E+02 kJ/mol Global net ELEC energy = 1.149444369079E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31821.7895436 RESULT 36589.03543806 RESULT 8468.632740499 RESULT 9996.323108319 RESULT 23233.56752071 RESULT 26477.76789284 RESULT 114.9444369079 Testing computed result 3.182178954360E+04 against expected result 3.182179E+04 *** PASSED *** Testing computed result 3.658903543806E+04 against expected result 3.658904E+04 *** PASSED *** Testing computed result 8.468632740499E+03 against expected result 8.468633E+03 *** PASSED *** Testing computed result 9.996323108319E+03 against expected result 9.996323E+03 *** PASSED *** Testing computed result 2.323356752071E+04 against expected result 2.323357E+04 *** PASSED *** Testing computed result 2.647776789284E+04 against expected result 2.647777E+04 *** PASSED *** Testing computed result 1.149444369079E+02 against expected result 1.149444E+02 *** PASSED *** Elapsed time: 52.043933 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.275.in BINARY: apbs INPUT: apbs-0.275.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.275.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.182051070674E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.275.dx Ion number density to be written to ndens-complex-0.275.dx Total electrostatic energy = 3.658775551975E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.275-PE0.dx Writing number density to ndens-complex-0.275-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.468218414737E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.275.dx Ion number density to be written to ndens-pep-0.275.dx Total electrostatic energy = 9.995910367297E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.275-PE0.dx Writing number density to ndens-pep-0.275-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.323168374787E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.85617 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.275 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.275 M concentration 2.000 A-radius, -1.000 e-charge, 0.275 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.275.dx Ion number density to be written to ndens-rna-0.275.dx Total electrostatic energy = 2.647588345522E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.275-PE0.dx Writing number density to ndens-rna-0.275-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.159616972338E+02 kJ/mol Global net ELEC energy = 1.159616972338E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31820.51070674 RESULT 36587.75551975 RESULT 8468.218414737 RESULT 9995.910367297 RESULT 23231.68374787 RESULT 26475.88345522 RESULT 115.9616972338 Testing computed result 3.182051070674E+04 against expected result 3.182051E+04 *** PASSED *** Testing computed result 3.658775551975E+04 against expected result 3.658776E+04 *** PASSED *** Testing computed result 8.468218414737E+03 against expected result 8.468218E+03 *** PASSED *** Testing computed result 9.995910367297E+03 against expected result 9.995910E+03 *** PASSED *** Testing computed result 2.323168374787E+04 against expected result 2.323168E+04 *** PASSED *** Testing computed result 2.647588345522E+04 against expected result 2.647588E+04 *** PASSED *** Testing computed result 1.159616972338E+02 against expected result 1.159617E+02 *** PASSED *** Elapsed time: 53.918413 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.300.in BINARY: apbs INPUT: apbs-0.300.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.300.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181936493519E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.300.dx Ion number density to be written to ndens-complex-0.300.dx Total electrostatic energy = 3.658660893678E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.300-PE0.dx Writing number density to ndens-complex-0.300-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.467838971928E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.300.dx Ion number density to be written to ndens-pep-0.300.dx Total electrostatic energy = 9.995532397856E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.300-PE0.dx Writing number density to ndens-pep-0.300-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.322999676177E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.60685 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.300 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.300 M concentration 2.000 A-radius, -1.000 e-charge, 0.300 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.300.dx Ion number density to be written to ndens-rna-0.300.dx Total electrostatic energy = 2.647419611346E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.300-PE0.dx Writing number density to ndens-rna-0.300-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.168804254687E+02 kJ/mol Global net ELEC energy = 1.168804254687E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31819.36493519 RESULT 36586.60893678 RESULT 8467.838971928 RESULT 9995.532397856 RESULT 23229.99676177 RESULT 26474.19611346 RESULT 116.8804254687 Testing computed result 3.181936493519E+04 against expected result 3.181936E+04 *** PASSED *** Testing computed result 3.658660893678E+04 against expected result 3.658661E+04 *** PASSED *** Testing computed result 8.467838971928E+03 against expected result 8.467839E+03 *** PASSED *** Testing computed result 9.995532397856E+03 against expected result 9.995532E+03 *** PASSED *** Testing computed result 2.322999676177E+04 against expected result 2.323000E+04 *** PASSED *** Testing computed result 2.647419611346E+04 against expected result 2.647420E+04 *** PASSED *** Testing computed result 1.168804254687E+02 against expected result 1.168804E+02 *** PASSED *** Elapsed time: 55.321795 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.325.in BINARY: apbs INPUT: apbs-0.325.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.325.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181832869046E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.325.dx Ion number density to be written to ndens-complex-0.325.dx Total electrostatic energy = 3.658557208654E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.325-PE0.dx Writing number density to ndens-complex-0.325-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.467489074881E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.325.dx Ion number density to be written to ndens-pep-0.325.dx Total electrostatic energy = 9.995183878464E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.325-PE0.dx Writing number density to ndens-pep-0.325-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.322847209567E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 5.38689 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.325 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.325 M concentration 2.000 A-radius, -1.000 e-charge, 0.325 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.325.dx Ion number density to be written to ndens-rna-0.325.dx Total electrostatic energy = 2.647267132259E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.325-PE0.dx Writing number density to ndens-rna-0.325-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.177168854907E+02 kJ/mol Global net ELEC energy = 1.177168854907E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31818.32869046 RESULT 36585.57208654 RESULT 8467.489074881 RESULT 9995.183878464 RESULT 23228.47209567 RESULT 26472.67132259 RESULT 117.7168854907 Testing computed result 3.181832869046E+04 against expected result 3.181833E+04 *** PASSED *** Testing computed result 3.658557208654E+04 against expected result 3.658557E+04 *** PASSED *** Testing computed result 8.467489074881E+03 against expected result 8.467489E+03 *** PASSED *** Testing computed result 9.995183878464E+03 against expected result 9.995184E+03 *** PASSED *** Testing computed result 2.322847209567E+04 against expected result 2.322847E+04 *** PASSED *** Testing computed result 2.647267132259E+04 against expected result 2.647267E+04 *** PASSED *** Testing computed result 1.177168854907E+02 against expected result 1.177169E+02 *** PASSED *** Elapsed time: 55.017817 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.400.in BINARY: apbs INPUT: apbs-0.400.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.400.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181571629593E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.400.dx Ion number density to be written to ndens-complex-0.400.dx Total electrostatic energy = 3.658295870300E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.400-PE0.dx Writing number density to ndens-complex-0.400-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.466578740909E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.400.dx Ion number density to be written to ndens-pep-0.400.dx Total electrostatic energy = 9.994277216885E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.400-PE0.dx Writing number density to ndens-pep-0.400-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.322463613929E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.85568 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.400 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.400 M concentration 2.000 A-radius, -1.000 e-charge, 0.400 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.400.dx Ion number density to be written to ndens-rna-0.400.dx Total electrostatic energy = 2.646883588223E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.400-PE0.dx Writing number density to ndens-rna-0.400-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.198456038802E+02 kJ/mol Global net ELEC energy = 1.198456038802E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31815.71629593 RESULT 36582.958703 RESULT 8466.578740909 RESULT 9994.277216885 RESULT 23224.63613929 RESULT 26468.83588223 RESULT 119.8456038802 Testing computed result 3.181571629593E+04 against expected result 3.181572E+04 *** PASSED *** Testing computed result 3.658295870300E+04 against expected result 3.658296E+04 *** PASSED *** Testing computed result 8.466578740909E+03 against expected result 8.466579E+03 *** PASSED *** Testing computed result 9.994277216885E+03 against expected result 9.994277E+03 *** PASSED *** Testing computed result 2.322463613929E+04 against expected result 2.322464E+04 *** PASSED *** Testing computed result 2.646883588223E+04 against expected result 2.646884E+04 *** PASSED *** Testing computed result 1.198456038802E+02 against expected result 1.198456E+02 *** PASSED *** Elapsed time: 54.874001 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.500.in BINARY: apbs INPUT: apbs-0.500.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.500.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181302243781E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.500.dx Ion number density to be written to ndens-complex-0.500.dx Total electrostatic energy = 3.658026461575E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.500-PE0.dx Writing number density to ndens-complex-0.500-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.465598755475E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.500.dx Ion number density to be written to ndens-pep-0.500.dx Total electrostatic energy = 9.993301332440E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.500-PE0.dx Writing number density to ndens-pep-0.500-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.322070101887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.34305 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.500 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.500 M concentration 2.000 A-radius, -1.000 e-charge, 0.500 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.500.dx Ion number density to be written to ndens-rna-0.500.dx Total electrostatic energy = 2.646490251594E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.500-PE0.dx Writing number density to ndens-rna-0.500-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.220607673699E+02 kJ/mol Global net ELEC energy = 1.220607673699E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31813.02243781 RESULT 36580.26461575 RESULT 8465.598755475 RESULT 9993.30133244 RESULT 23220.70101887 RESULT 26464.90251594 RESULT 122.0607673699 Testing computed result 3.181302243781E+04 against expected result 3.181302E+04 *** PASSED *** Testing computed result 3.658026461575E+04 against expected result 3.658026E+04 *** PASSED *** Testing computed result 8.465598755475E+03 against expected result 8.465599E+03 *** PASSED *** Testing computed result 9.993301332440E+03 against expected result 9.993301E+03 *** PASSED *** Testing computed result 2.322070101887E+04 against expected result 2.322070E+04 *** PASSED *** Testing computed result 2.646490251594E+04 against expected result 2.646490E+04 *** PASSED *** Testing computed result 1.220607673699E+02 against expected result 1.220608E+02 *** PASSED *** Elapsed time: 55.083792 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.600.in BINARY: apbs INPUT: apbs-0.600.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.600.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.181090090954E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.600.dx Ion number density to be written to ndens-complex-0.600.dx Total electrostatic energy = 3.657814345443E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.600-PE0.dx Writing number density to ndens-complex-0.600-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.464799341688E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.600.dx Ion number density to be written to ndens-pep-0.600.dx Total electrostatic energy = 9.992505379555E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.600-PE0.dx Writing number density to ndens-pep-0.600-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.321762631365E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.96464 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.600 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.600 M concentration 2.000 A-radius, -1.000 e-charge, 0.600 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.600.dx Ion number density to be written to ndens-rna-0.600.dx Total electrostatic energy = 2.646183001839E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.600-PE0.dx Writing number density to ndens-rna-0.600-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.238080564885E+02 kJ/mol Global net ELEC energy = 1.238080564885E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31810.90090954 RESULT 36578.14345443 RESULT 8464.799341688 RESULT 9992.505379555 RESULT 23217.62631365 RESULT 26461.83001839 RESULT 123.8080564885 Testing computed result 3.181090090954E+04 against expected result 3.181090E+04 *** PASSED *** Testing computed result 3.657814345443E+04 against expected result 3.657814E+04 *** PASSED *** Testing computed result 8.464799341688E+03 against expected result 8.464799E+03 *** PASSED *** Testing computed result 9.992505379555E+03 against expected result 9.992505E+03 *** PASSED *** Testing computed result 2.321762631365E+04 against expected result 2.321763E+04 *** PASSED *** Testing computed result 2.646183001839E+04 against expected result 2.646183E+04 *** PASSED *** Testing computed result 1.238080564885E+02 against expected result 1.238081E+02 *** PASSED *** Elapsed time: 53.751562 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.700.in BINARY: apbs INPUT: apbs-0.700.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.700.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.180915789156E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.700.dx Ion number density to be written to ndens-complex-0.700.dx Total electrostatic energy = 3.657640108752E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.700-PE0.dx Writing number density to ndens-complex-0.700-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.464126109756E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.700.dx Ion number density to be written to ndens-pep-0.700.dx Total electrostatic energy = 9.991835140855E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.700-PE0.dx Writing number density to ndens-pep-0.700-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.321512352191E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.67055 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.700 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.700 M concentration 2.000 A-radius, -1.000 e-charge, 0.700 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.700.dx Ion number density to be written to ndens-rna-0.700.dx Total electrostatic energy = 2.645932953757E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.700-PE0.dx Writing number density to ndens-rna-0.700-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.252364090878E+02 kJ/mol Global net ELEC energy = 1.252364090878E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31809.15789156 RESULT 36576.40108752 RESULT 8464.126109756 RESULT 9991.835140855 RESULT 23215.12352191 RESULT 26459.32953757 RESULT 125.2364090878 Testing computed result 3.180915789156E+04 against expected result 3.180916E+04 *** PASSED *** Testing computed result 3.657640108752E+04 against expected result 3.657640E+04 *** PASSED *** Testing computed result 8.464126109756E+03 against expected result 8.464126E+03 *** PASSED *** Testing computed result 9.991835140855E+03 against expected result 9.991835E+03 *** PASSED *** Testing computed result 2.321512352191E+04 against expected result 2.321512E+04 *** PASSED *** Testing computed result 2.645932953757E+04 against expected result 2.645933E+04 *** PASSED *** Testing computed result 1.252364090878E+02 against expected result 1.252364E+02 *** PASSED *** Elapsed time: 55.979888 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-0.800.in BINARY: apbs INPUT: apbs-0.800.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 23 2020 at 09:35:23 Parsing input file apbs-0.800.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from model_outNB.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 998 atoms Centered at (1.382e+01, 5.283e+00, 8.258e+00) Net charge -1.40e+01 e Reading PQR-format atom data from model_outNpep.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 379 atoms Centered at (1.753e+01, -1.723e+00, 1.470e+01) Net charge 4.00e+00 e Reading PQR-format atom data from model_outBoxB19.pqr. 619 atoms Centered at (1.306e+01, 7.586e+00, 4.177e+00) Net charge -1.80e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 215.815 MB total, 215.815 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.180768241803E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 215.815 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-complex-0.800.dx Ion number density to be written to ndens-complex-0.800.dx Total electrostatic energy = 3.657492640520E+04 kJ/mol Calculating forces... Writing charge density to qdens-complex-0.800-PE0.dx Writing number density to ndens-complex-0.800-PE0.dx ---------------------------------------- CALCULATION #3 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.463546035019E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (peptide): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 200.178 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-pep-0.800.dx Ion number density to be written to ndens-pep-0.800.dx Total electrostatic energy = 9.991257699113E+03 kJ/mol Calculating forces... Writing charge density to qdens-pep-0.800-PE0.dx Writing number density to ndens-pep-0.800-PE0.dx ---------------------------------------- CALCULATION #5 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.572 x 0.643 Grid lengths: 45.332 x 54.950 x 82.263 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.321302636223E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (rna): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 3.43348 A Current memory usage: 208.541 MB total, 428.140 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 97 x 129 Grid spacings: 0.708 x 0.545 x 0.534 Grid lengths: 45.332 x 52.323 x 68.390 Grid center: (13.822, 5.283, 8.258) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.800 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.800 M concentration 2.000 A-radius, -1.000 e-charge, 0.800 M concentration Solute dielectric: 4.000 Solvent dielectric: 80.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Ion charge density to be written to qdens-rna-0.800.dx Ion number density to be written to ndens-rna-0.800.dx Total electrostatic energy = 2.645723464562E+04 kJ/mol Calculating forces... Writing charge density to qdens-rna-0.800-PE0.dx Writing number density to ndens-rna-0.800-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 1 (complex) - 2 (peptide) - 3 (rna) end Local net energy (PE 0) = 1.264340604647E+02 kJ/mol Global net ELEC energy = 1.264340604647E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 428.140 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-0.out RESULT 31807.68241803 RESULT 36574.9264052 RESULT 8463.546035019 RESULT 9991.257699113 RESULT 23213.02636223 RESULT 26457.23464562 RESULT 126.4340604647 Testing computed result 3.180768241803E+04 against expected result 3.180768E+04 *** PASSED *** Testing computed result 3.657492640520E+04 against expected result 3.657493E+04 *** PASSED *** Testing computed result 8.463546035019E+03 against expected result 8.463546E+03 *** PASSED *** Testing computed result 9.991257699113E+03 against expected result 9.991258E+03 *** PASSED *** Testing computed result 2.321302636223E+04 against expected result 2.321303E+04 *** PASSED *** Testing computed result 2.645723464562E+04 against expected result 2.645723E+04 *** PASSED *** Testing computed result 1.264340604647E+02 against expected result 1.264341E+02 *** PASSED *** Elapsed time: 56.832779 seconds -------------------------------------------------------------------------------- Total elapsed time: 952.663558 seconds Test results have been logged -------------------------------------------------------------------------------- make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 dh_testroot dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install --sourcedir=apbs --destdir=/<>/debian/tmp/ cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/<>/apbs-3.0.0\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/apbs -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/debian/tmp/usr/share/apbs/doc -- Installing: /<>/debian/tmp/usr/share/apbs/doc/ChangeLog.md -- Installing: /<>/debian/tmp/usr/share/apbs/doc/README -- Installing: /<>/debian/tmp/usr/share/apbs/doc/icons -- Installing: /<>/debian/tmp/usr/share/apbs/doc/icons/APBS_512.png -- Installing: /<>/debian/tmp/usr/share/apbs/doc/icons/APBS_128_v2.png -- Installing: /<>/debian/tmp/usr/share/apbs/doc/icons/APBS_16.png -- Installing: /<>/debian/tmp/usr/share/apbs/doc/icons/APBS_128.png -- Installing: /<>/debian/tmp/usr/share/apbs/doc/icons/APBS_32.png -- Installing: /<>/debian/tmp/usr/share/apbs/doc/icons/APBS_256.png -- Installing: /<>/debian/tmp/usr/share/apbs/doc/icons/APBS_1024.png -- Installing: /<>/debian/tmp/usr/share/apbs/doc/icons/APBS_64.png -- Installing: /<>/debian/tmp/usr/share/apbs/doc/data-ontology -- Installing: /<>/debian/tmp/usr/share/apbs/doc/data-ontology/protege.sh -- Installing: /<>/debian/tmp/usr/share/apbs/doc/data-ontology/catalog-v001.xml -- Installing: /<>/debian/tmp/usr/share/apbs/doc/data-ontology/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/doc/data-ontology/data-ontology.ttl -- Installing: /<>/debian/tmp/usr/share/apbs/doc/ReleaseNotes.md -- Installing: /<>/debian/tmp/usr/share/apbs/doc/release_procedure.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/apbs-PDB.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/fas2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/mache.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/achbp.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/force.result -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/apbs-forces.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/mol.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/2-methylbutane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/cyclohexane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/methane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/isobutane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/cyclopentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/butane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/neopentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/pentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/ethane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/hexane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/propane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-vdw.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-surf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_bin_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-surf.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-apo.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-bin.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/README -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-apo.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-lig.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-bin.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_apo_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-vdw.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-surf.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-vdw.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-surf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-vdw.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/runme.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/complex.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/polarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/apolarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/opal -- Installing: /<>/debian/tmp/usr/share/apbs/examples/opal/actin-dimer.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/opal/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/opal/actin-mol2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/opal/born.xml -- Installing: /<>/debian/tmp/usr/share/apbs/examples/opal/actin-mol1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/opal/actin-complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/opal/actin-dimer-para.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.500-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.800.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.225-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.075-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.150-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.275-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.800-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.250-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.125-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.600-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.225-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.300-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.325-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.250-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.175-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.225-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.700.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.300.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.500-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.400-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.025-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.025-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.075-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.200-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.200.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.600.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.250.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outBoxB19.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.075.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.200-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.125-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.500.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.125-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.700-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.075.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.400-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.025-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.100-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.125-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.700.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.300.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.700-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNpep.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.175-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.275.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.050-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.300-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.700-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.275-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.125.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.025-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.225-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.050-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.100.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.100-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.700-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/run_apdx_files.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.400-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.275-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.500.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.175-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.100-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.800-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.600-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.075-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.400-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/template.txt -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.700-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.125.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.300-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.300-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.800.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.700-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.025.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outBoxB19.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNpep.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNB.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.100-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.400.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.200-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.225-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.175-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.050.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.400-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath.txt -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.600-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.050-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.500-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.100-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.175.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.150-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.275-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.225-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.600-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNB.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.200-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.325.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.050-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.600.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.400.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.325-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/fit.py -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.100.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.250-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.125-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.150-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.800-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.150-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.150-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/test.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.800-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.250-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.500-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.150-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.125-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.225.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.250.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.325-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.500-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.300-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.075-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.175-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.175.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.275.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.025.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.250-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.600-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.600-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/postprocess.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.175-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs_dx.py -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.250-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.150.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.025-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.150.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.325-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.325.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath-0.225.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.800-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.400-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-rna-0.325-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.275-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.275-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.050.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.200.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.200-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.050-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.025-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.050-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-rna-0.100-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.200-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.075-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-complex-0.075-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-complex-0.300-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/qdens-pep-0.325-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.500-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs-0.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/ndens-pep-0.800-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/acet.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-mol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/hca.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.err -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/srsrf.dot -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.err -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf1.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel-PE1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel-PE2.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-fem.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem-extmesh.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-forces.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel-PE2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel-PE1.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/pmf.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel-PE1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel-PE0.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel-PE0.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel-PE0.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel-PE0.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel-PE2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/ion.xml -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel-PE3.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-auto.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-apolar.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/polarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apolarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-auto.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel-PE1.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel-PE2.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel-PE3.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel-PE3.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/ion.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel-PE3.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barnase.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barstar.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barn_bars_electro.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/451c.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1ajj.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/oneb.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1bbl.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/1a63_msms.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/451c_order1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/451c_order5.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_SES.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_Skin.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_3.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_3.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_energyforce.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_charge.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_dynamics.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_charge.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/1a63.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/apbs-mol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.dat.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.out.orig.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.inp.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.pdb.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/proton.xml -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetic-acid.xml -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/proton.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/apbs-smol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetate.xml -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetic-acid.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetate.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_dynamics.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_energyforce.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE6.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE5.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE6.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE4.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE2.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE4.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE5.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE7.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE4.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE1.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/pot-PE0.dx -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE0.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE5.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.full.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot4.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot3.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/srsrf.dot -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/single.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE0.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE0.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE7.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE4.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE0.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE6.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE5.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE3.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-auto.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE6.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-auto.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE7.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE1.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE7.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE2.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel-PE3.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE3.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel-PE3.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASP66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/ASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/ASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/methanol.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.dat.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.inp.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.out.orig.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/methoxide.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/small491.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/491.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.e2.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel12.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel12.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/491.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/runme.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/point-pmf-0.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/energy.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol0.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol3.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/dmso-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/io.mc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/dss-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-smol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole_zap.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/glycerol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/smpbe -- Installing: /<>/debian/tmp/usr/share/apbs/examples/smpbe/readme.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/smpbe/24dup.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/smpbe/apbs-smpbe-24dup.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/smpbe/apbs-smpbe-ion.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/smpbe/ion.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-0.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Run_membrane-helix.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-12.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-8.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/draw_membrane2.c -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_solv-TEMPLATE.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-16.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/membrane -- Installing: /<>/debian/tmp/usr/share/apbs/examples/membrane/readme.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/membrane/memv.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/membrane/pot.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/tests -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_logger.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_results.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_intermediate_energies.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/test_cases.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_tester.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_forces.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_512x512@2x.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_16x16.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_256x256.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_32x32.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_128x128.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_16x16@2x.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_32x32@2x.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_128x128@2x.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_512x512.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/APBS.iconset/icon_256x256@2x.png -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/patch_binary.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/info.plist -- Installing: /<>/debian/tmp/usr/share/apbs/tools/osx/apbs_term -- Installing: /<>/debian/tmp/usr/share/apbs/tools/README.html -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/WHATIF2AMBER.sed -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/qcd2pqr.awk -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.xml -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber2uhbd.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/c-alpha.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber-param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/weiner86-param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/amber2charmm.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/configuration headers -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/configuration headers/apbscfg.h -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/configuration headers/maloccf.h -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/README.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/command-line support -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/command-line support/apbs-cli.bat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/visual studio property pages -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/visual studio property pages/Release build properties.props -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/visual studio property pages/Generic build properties.props -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/visual studio property pages/Debug build properties.props -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/NSI configuration -- Installing: /<>/debian/tmp/usr/share/apbs/tools/windows/NSI configuration/apbs.nsi -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib.i -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib_wrap.doc -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/README -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/mergedx.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/README -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgridlib.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.i -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/read.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/average.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/noinput.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/main.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/ion.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github/release-data.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github/getReleases.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cm -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cm -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/del2dx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mergedx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/multivalue.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mergedx2.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dx2uhbd.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/analysis.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/benchmark.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/value.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/smooth.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dxmath.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/similarity.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/uhbd_asc2bin.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/tensor2dx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dx2mol.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mgmesh.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/inputgen.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/psize.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/__pycache__ -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/__pycache__/psize.cpython-38.pyc -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/__pycache__/inputgen.cpython-38.pyc -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/born.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/coulomb.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dx2mol -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/similarity -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mergedx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/tensor2dx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/analysis -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/born -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/del2dx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/value -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/benchmark -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mgmesh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dxmath -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/coulomb -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_routines.so.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_routines.so -- Installing: /<>/debian/tmp/usr/include/apbs/apbs.h -- Installing: /<>/debian/tmp/usr/include/apbs/routines.h -- Installing: /<>/debian/tmp/usr/bin/apbs -- Installing: /<>/debian/tmp/usr/include/apbs/generic/nosh.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/mgparm.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/femparm.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/pbamparm.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/pbsamparm.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/pbeparm.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/bemparm.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/geoflowparm.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/apolparm.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vacc.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/valist.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vatom.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vpbe.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vcap.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vclist.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vstring.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vparam.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vgreen.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vmatrix.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vhal.h -- Installing: /<>/debian/tmp/usr/include/apbs/generic/vunit.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_generic.so.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_generic.so -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/buildAd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/buildBd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/buildGd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/buildPd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/cgd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/gsd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/matvecd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/mgcsd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/mgdrvd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/mgsubd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/mikpckd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/mlinpckd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/mypdec.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/newtond.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/newdrvd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/powerd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/smoothd.h -- Installing: /<>/debian/tmp/usr/include/apbs/pmgc/mgfasd.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_pmgc.so.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_pmgc.so -- Installing: /<>/debian/tmp/usr/include/apbs/mg/vgrid.h -- Installing: /<>/debian/tmp/usr/include/apbs/mg/vmgrid.h -- Installing: /<>/debian/tmp/usr/include/apbs/mg/vopot.h -- Installing: /<>/debian/tmp/usr/include/apbs/mg/vpmg.h -- Installing: /<>/debian/tmp/usr/include/apbs/mg/vpmgp.h -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_mg.so.3 -- Installing: /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libapbs_mg.so make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[1]: Leaving directory '/<>' dh_install dh_installdocs dh_installchangelogs dh_installman dh_python3 I: dh_python3 fs:343: renaming _apbslib.so to _apbslib.cpython-38-x86_64-linux-gnu.so dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-indep make[1]: Entering directory '/<>' dh_fixperms for example in FKBP/1d7h-dmso/UHBD/pqr2qcd \ ion-pmf/runme.sh \ point-pmf/runme.sh \ protein-rna/postprocess.sh \ protein-rna/test.sh \ helix/Run_membrane-helix.sh \ protein-rna/run_apdx_files.sh; \ do \ chmod +x debian/apbs-data/usr/share/apbs/examples/${example}; \ done for script in amber2charmm.sh \ param/pdb2pqr/amber2uhbd.sh \ qcd2pqr.awk; \ do \ chmod a+x debian/apbs-data/usr/share/apbs/tools/conversion/${script}; \ done make[1]: Leaving directory '/<>' dh_fixperms -Napbs-data dh_missing dh_dwz -a dwz: debian/libapbs3/usr/lib/x86_64-linux-gnu/libapbs_pmgc.so.3: DWARF compression not beneficial - old size 145118 new size 145920 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libapbs3/usr/lib/x86_64-linux-gnu/libapbs_generic.so.3 was not linked against libpthread.so.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb were not linked against libapbs_pmgc.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb were not linked against libmpi.so.40 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs was not linked against libapbs_routines.so.3 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb were not linked against libstdc++.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb were not linked against libpthread.so.0 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/bin/value debian/apbs/usr/lib/apbs/tools/bin/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/bin/born debian/apbs/usr/lib/apbs/tools/bin/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/bin/coulomb were not linked against libgomp.so.1 (they use none of the library's symbols) dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libapbs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-apbslib: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-apbslib: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-apbslib: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-apbslib: substitution variable ${python3:Versions} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.0.0+dfsg1-3_amd64.deb'. dpkg-deb: building package 'libapbs3-dbgsym' in '../libapbs3-dbgsym_3.0.0+dfsg1-3_amd64.deb'. dpkg-deb: building package 'apbs' in '../apbs_3.0.0+dfsg1-3_amd64.deb'. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.0.0+dfsg1-3_amd64.deb'. dpkg-deb: building package 'apbs-dbgsym' in '../apbs-dbgsym_3.0.0+dfsg1-3_amd64.deb'. dpkg-deb: building package 'libapbs3' in '../libapbs3_3.0.0+dfsg1-3_amd64.deb'. dpkg-deb: building package 'apbs-data' in '../apbs-data_3.0.0+dfsg1-3_all.deb'. dpkg-deb: building package 'python3-apbslib-dbgsym' in '../python3-apbslib-dbgsym_3.0.0+dfsg1-3_amd64.deb'. dpkg-genbuildinfo dpkg-genchanges >../apbs_3.0.0+dfsg1-3_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2020-10-03T00:29:39Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ apbs_3.0.0+dfsg1-3_amd64.changes: --------------------------------- Format: 1.8 Date: Thu, 23 Jul 2020 17:35:23 +0800 Source: apbs Binary: apbs apbs-data apbs-dbgsym libapbs-dev libapbs3 libapbs3-dbgsym python3-apbslib python3-apbslib-dbgsym Architecture: source all amd64 Version: 3.0.0+dfsg1-3 Distribution: sid Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Description: apbs - Adaptive Poisson Boltzmann Solver apbs-data - data files for APBS (Adaptive Poisson Boltzmann Solver) libapbs-dev - Adaptive Poisson Boltzmann Solver libapbs3 - Adaptive Poisson Boltzmann Solver python3-apbslib - Adaptive Poisson Boltzmann Solver Closes: 956998 Changes: apbs (3.0.0+dfsg1-3) unstable; urgency=medium . * Team upload. * use -fcommon in CFLAGS to aid build with gcc-10 (managing multiple definitions of common variables). Closes: #956998. * provide python path to inputgen for build-time tests Checksums-Sha1: 0198cd48e7c0cf77536976bcaf155527a03be611 1409 apbs_3.0.0+dfsg1-3.dsc 7fd00c61349ff3e8d4e912871d6b9066b2ef3c50 14280 apbs_3.0.0+dfsg1-3.debian.tar.xz a7689c190f2826fa9a22e83422b5aa35fb59b1b1 226122852 apbs-data_3.0.0+dfsg1-3_all.deb d29d51a64695a2cad4e417f598864e3b3285c83a 155644 apbs-dbgsym_3.0.0+dfsg1-3_amd64.deb 6db5b02713729eb3de11c4edea88709ba2507131 10086 apbs_3.0.0+dfsg1-3_amd64.buildinfo 98252d7ae73270e96948ce24ff0643c817dfc0cc 86180 apbs_3.0.0+dfsg1-3_amd64.deb 1a6ce88219630661631421ee0c7d3cebd9374c5e 66316 libapbs-dev_3.0.0+dfsg1-3_amd64.deb 7f84b2eb9a71b074fbd8321de1ded69e75ae094c 548416 libapbs3-dbgsym_3.0.0+dfsg1-3_amd64.deb 06ee20010ade85bc683f3cdacdc44944bc1ba32e 246280 libapbs3_3.0.0+dfsg1-3_amd64.deb 3f3b3784a398fa0eebd4e9db57f20b4344ae5da7 158692 python3-apbslib-dbgsym_3.0.0+dfsg1-3_amd64.deb c06b55efcc9a60173f1ff89e605362cb6a8a82a7 103932 python3-apbslib_3.0.0+dfsg1-3_amd64.deb Checksums-Sha256: f69a91866644ad52e3a56568c49bc229226042120f682a29653335f011e812a0 1409 apbs_3.0.0+dfsg1-3.dsc c9573aab7b2d26f4925c82a597bf4658c33dab324a99f245c46247cb8f43ca37 14280 apbs_3.0.0+dfsg1-3.debian.tar.xz ad1c7d85b866d75b5c8582108f40db477421aee07876f6d92a1803f3c7e662af 226122852 apbs-data_3.0.0+dfsg1-3_all.deb aedce209e24605852392ed4cdb76144ba1e38a211f0de20e3cbfa16846136a7c 155644 apbs-dbgsym_3.0.0+dfsg1-3_amd64.deb ec6c060c8bbf2a6e99902cf84f0f4b2614463cf72d2cce70a20cd5d211494706 10086 apbs_3.0.0+dfsg1-3_amd64.buildinfo 91df2f9587808c866b76d21d77a42a78e4485c3f2fdef1cc866f91638cedd879 86180 apbs_3.0.0+dfsg1-3_amd64.deb fb34edf40a932bafa108038389f9468b861615b8b2e8b80843449f6e8438f444 66316 libapbs-dev_3.0.0+dfsg1-3_amd64.deb dbf90d31e6a040490b2570183334f4857b8ab303c6f80737e5461d3541ecfbad 548416 libapbs3-dbgsym_3.0.0+dfsg1-3_amd64.deb 64dc92ad8e67d9c8cd2123f2f722662a3837e12149b4fd761edeb3196a435156 246280 libapbs3_3.0.0+dfsg1-3_amd64.deb d843cc6ff8558d03fb46690c9145e45ee2b5cac4f80ca12412d73d333eda265a 158692 python3-apbslib-dbgsym_3.0.0+dfsg1-3_amd64.deb 9d3f2fb40f29e2f7ab9d3710a7a49857853bb857a296d7edb4088ee30d81593c 103932 python3-apbslib_3.0.0+dfsg1-3_amd64.deb Files: df4701ad63176cd891b3d1e4e721960a 1409 science optional apbs_3.0.0+dfsg1-3.dsc 6c5ce01351dda9673668ca8af404f631 14280 science optional apbs_3.0.0+dfsg1-3.debian.tar.xz 069d05a3f84369bc3336aa4369f8c33e 226122852 science optional apbs-data_3.0.0+dfsg1-3_all.deb e7adba87c21ef378cea16454b8c24dab 155644 debug optional apbs-dbgsym_3.0.0+dfsg1-3_amd64.deb d88a2fca1bef53fc6f17d151ceeadbf1 10086 science optional apbs_3.0.0+dfsg1-3_amd64.buildinfo e0f482523b483cddcb25e87beda6cd59 86180 science optional apbs_3.0.0+dfsg1-3_amd64.deb e19dc8c906029323e8d574f5314cded1 66316 libdevel optional libapbs-dev_3.0.0+dfsg1-3_amd64.deb 84d900ca551379e5acffc96b8521d622 548416 debug optional libapbs3-dbgsym_3.0.0+dfsg1-3_amd64.deb fff68e30645c37419842e583239f78f7 246280 libs optional libapbs3_3.0.0+dfsg1-3_amd64.deb ffbc697ec9a9e8fc585982490fc186ac 158692 debug optional python3-apbslib-dbgsym_3.0.0+dfsg1-3_amd64.deb d0cff24d84443ccc24790a5d4df9d4f1 103932 python optional python3-apbslib_3.0.0+dfsg1-3_amd64.deb /<>/apbs_3.0.0+dfsg1-3_amd64.changes.new could not be renamed to /<>/apbs_3.0.0+dfsg1-3_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: apbs Binary: apbs apbs-data apbs-dbgsym libapbs-dev libapbs3 libapbs3-dbgsym python3-apbslib python3-apbslib-dbgsym Architecture: all amd64 source Version: 3.0.0+dfsg1-3 Checksums-Md5: df4701ad63176cd891b3d1e4e721960a 1409 apbs_3.0.0+dfsg1-3.dsc 069d05a3f84369bc3336aa4369f8c33e 226122852 apbs-data_3.0.0+dfsg1-3_all.deb e7adba87c21ef378cea16454b8c24dab 155644 apbs-dbgsym_3.0.0+dfsg1-3_amd64.deb 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06ee20010ade85bc683f3cdacdc44944bc1ba32e 246280 libapbs3_3.0.0+dfsg1-3_amd64.deb 3f3b3784a398fa0eebd4e9db57f20b4344ae5da7 158692 python3-apbslib-dbgsym_3.0.0+dfsg1-3_amd64.deb c06b55efcc9a60173f1ff89e605362cb6a8a82a7 103932 python3-apbslib_3.0.0+dfsg1-3_amd64.deb Checksums-Sha256: f69a91866644ad52e3a56568c49bc229226042120f682a29653335f011e812a0 1409 apbs_3.0.0+dfsg1-3.dsc ad1c7d85b866d75b5c8582108f40db477421aee07876f6d92a1803f3c7e662af 226122852 apbs-data_3.0.0+dfsg1-3_all.deb aedce209e24605852392ed4cdb76144ba1e38a211f0de20e3cbfa16846136a7c 155644 apbs-dbgsym_3.0.0+dfsg1-3_amd64.deb 91df2f9587808c866b76d21d77a42a78e4485c3f2fdef1cc866f91638cedd879 86180 apbs_3.0.0+dfsg1-3_amd64.deb fb34edf40a932bafa108038389f9468b861615b8b2e8b80843449f6e8438f444 66316 libapbs-dev_3.0.0+dfsg1-3_amd64.deb dbf90d31e6a040490b2570183334f4857b8ab303c6f80737e5461d3541ecfbad 548416 libapbs3-dbgsym_3.0.0+dfsg1-3_amd64.deb 64dc92ad8e67d9c8cd2123f2f722662a3837e12149b4fd761edeb3196a435156 246280 libapbs3_3.0.0+dfsg1-3_amd64.deb d843cc6ff8558d03fb46690c9145e45ee2b5cac4f80ca12412d73d333eda265a 158692 python3-apbslib-dbgsym_3.0.0+dfsg1-3_amd64.deb 9d3f2fb40f29e2f7ab9d3710a7a49857853bb857a296d7edb4088ee30d81593c 103932 python3-apbslib_3.0.0+dfsg1-3_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 03 Oct 2020 00:29:34 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.118), autoconf (= 2.69-11.1), automake (= 1:1.16.2-4), autopoint (= 0.19.8.1-10), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.47), bash (= 5.0-7), binutils (= 2.35.1-1), binutils-common (= 2.35.1-1), binutils-x86-64-linux-gnu (= 2.35.1-1), bsdextrautils (= 2.36-3+b1), bsdutils (= 1:2.36-3+b1), build-essential (= 12.8), bzip2 (= 1.0.8-4), cmake (= 3.18.2-1), cmake-data (= 3.18.2-1), coreutils (= 8.32-4+b1), cpp (= 4:10.2.0-1), cpp-10 (= 10.2.0-13), cpp-9 (= 9.3.0-18), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.2.1), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-python (= 4.20200925), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3), dpkg (= 1.20.5), dpkg-dev (= 1.20.5), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1), g++ (= 4:10.2.0-1), g++-10 (= 10.2.0-13), gcc (= 4:10.2.0-1), gcc-10 (= 10.2.0-13), gcc-10-base (= 10.2.0-13), gcc-9 (= 9.3.0-18), gcc-9-base (= 9.3.0-18), gettext (= 0.19.8.1-10), gettext-base (= 0.19.8.1-10), gfortran-9 (= 9.3.0-18), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2), hostname (= 3.23), ibverbs-providers (= 31.0-1), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.4.3-2), libasan5 (= 9.3.0-18), libasan6 (= 10.2.0-13), libatomic1 (= 10.2.0-13), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3), libaudit1 (= 1:2.8.5-3+b1), libbinutils (= 2.35.1-1), libblkid1 (= 2.36-3+b1), libbrotli1 (= 1.0.9-2), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-4), libc-bin (= 2.31-3), libc-dev-bin (= 2.31-3), libc6 (= 2.31-3), libc6-dev (= 2.31-3), libcap-ng0 (= 0.7.9-2.2), libcbor0 (= 0.5.0+dfsg-2), libcc1-0 (= 10.2.0-13), libcom-err2 (= 1.45.6-1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.17-1), libcrypt1 (= 1:4.4.17-1), libctf-nobfd0 (= 2.35.1-1), libctf0 (= 2.35.1-1), libcurl4 (= 7.72.0-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.254), libdebhelper-perl (= 13.2.1), libdpkg-perl (= 1.20.5), libedit2 (= 3.1-20191231-1), libelf1 (= 0.181-1), libevent-2.1-7 (= 2.1.12-stable-1), libevent-core-2.1-7 (= 2.1.12-stable-1), libevent-dev (= 2.1.12-stable-1), libevent-extra-2.1-7 (= 2.1.12-stable-1), libevent-openssl-2.1-7 (= 2.1.12-stable-1), libevent-pthreads-2.1-7 (= 2.1.12-stable-1), libexpat1 (= 2.2.9-1), libexpat1-dev (= 2.2.9-1), libfabric1 (= 1.11.0-2), libffi7 (= 3.3-4), libfido2-1 (= 1.5.0-2), libfile-stripnondeterminism-perl (= 1.9.0-1), libgcc-10-dev (= 10.2.0-13), libgcc-9-dev (= 9.3.0-18), libgcc-s1 (= 10.2.0-13), libgcrypt20 (= 1.8.6-2), libgdbm-compat4 (= 1.18.1-5.1), libgdbm6 (= 1.18.1-5.1), libgfortran-9-dev (= 9.3.0-18), libgfortran5 (= 10.2.0-13), libglib2.0-0 (= 2.66.0-2), libgmp10 (= 2:6.2.0+dfsg-6), libgnutls30 (= 3.6.15-4), libgomp1 (= 10.2.0-13), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.17-10), libhogweed6 (= 3.6-2), libhwloc-dev (= 2.3.0+dfsg-1), libhwloc-plugins (= 2.3.0+dfsg-1), libhwloc15 (= 2.3.0+dfsg-1), libibverbs-dev (= 31.0-1), libibverbs1 (= 31.0-1), libicu67 (= 67.1-4), libidn2-0 (= 2.3.0-1), libisl22 (= 0.22.1-1), libitm1 (= 10.2.0-13), libjs-jquery (= 3.5.1+dfsg-4), libjs-jquery-ui (= 1.12.1+dfsg-7), libjsoncpp1 (= 1.7.4-3.1), libk5crypto3 (= 1.17-10), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.17-10), libkrb5support0 (= 1.17-10), libldap-2.4-2 (= 2.4.53+dfsg-1), liblsan0 (= 10.2.0-13), libltdl-dev (= 2.4.6-14), libltdl7 (= 2.4.6-14), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmaloc-dev (= 1.5-1), libmaloc1 (= 1.5-1), libmount1 (= 2.36-3+b1), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.2+20200918-1), libncursesw6 (= 6.2+20200918-1), libnettle8 (= 3.6-2), libnghttp2-14 (= 1.41.0-3), libnl-3-200 (= 3.4.0-1+b1), libnl-3-dev (= 3.4.0-1+b1), libnl-route-3-200 (= 3.4.0-1+b1), libnl-route-3-dev (= 3.4.0-1+b1), libnuma-dev (= 2.0.12-1+b1), libnuma1 (= 2.0.12-1+b1), libopenmpi-dev (= 4.0.5-5), libopenmpi3 (= 4.0.5-5), libp11-kit0 (= 0.23.21-2), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpciaccess0 (= 0.16-1), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-13), libperl5.30 (= 5.30.3-4), libpipeline1 (= 1.5.3-1), libpmix-dev (= 3.2.0~rc1-4), libpmix2 (= 3.2.0~rc1-4), libprocps8 (= 2:3.3.16-5), libpsl5 (= 0.21.0-1.1), libpsm-infinipath1 (= 3.3+20.604758e7-6+b1), libpsm2-2 (= 11.2.185-1), libpython3-dev (= 3.8.2-3), libpython3-stdlib (= 3.8.2-3), libpython3.8 (= 3.8.6-1), libpython3.8-dev (= 3.8.6-1), libpython3.8-minimal (= 3.8.6-1), libpython3.8-stdlib (= 3.8.6-1), libquadmath0 (= 10.2.0-13), librdmacm1 (= 31.0-1), libreadline8 (= 8.0-4), librhash0 (= 1.4.0-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.27+dfsg-2), libsasl2-modules-db (= 2.1.27+dfsg-2), libseccomp2 (= 2.4.4-1), libselinux1 (= 3.1-2), libsemanage-common (= 3.1-1), libsemanage1 (= 3.1-1), libsepol1 (= 3.1-1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.36-3+b1), libsqlite3-0 (= 3.33.0-1), libssh2-1 (= 1.8.0-2.1), libssl1.1 (= 1.1.1g-1), libstdc++-10-dev (= 10.2.0-13), libstdc++6 (= 10.2.0-13), libsub-override-perl (= 0.09-2), libsystemd0 (= 246.6-1), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2+20200918-1), libtool (= 2.4.6-14), libtsan0 (= 10.2.0-13), libubsan1 (= 10.2.0-13), libuchardet0 (= 0.0.7-1), libucx0 (= 1.9.0~rc1-2), libudev1 (= 246.6-1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36-3+b1), libuv1 (= 1.39.0-1), libx11-6 (= 2:1.6.12-1), libx11-data (= 2:1.6.12-1), libxau6 (= 1:1.0.8-1+b2), libxcb1 (= 1.14-2), libxdmcp6 (= 1:1.1.2-3), libxext6 (= 2:1.3.3-1+b2), libxml2 (= 2.9.10+dfsg-6), libxnvctrl0 (= 450.66-1), libzstd1 (= 1.4.5+dfsg-4), linux-libc-dev (= 5.8.10-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.3-4), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), mime-support (= 3.64), mpi-default-dev (= 1.13), ncurses-base (= 6.2+20200918-1), ncurses-bin (= 6.2+20200918-1), node-jquery (= 3.5.1+dfsg-4), ocl-icd-libopencl1 (= 2.2.12-4), openmpi-bin (= 4.0.5-5), openmpi-common (= 4.0.5-5), openssh-client (= 1:8.3p1-1), passwd (= 1:4.8.1-1), patch (= 2.7.6-6), perl (= 5.30.3-4), perl-base (= 5.30.3-4), perl-modules-5.30 (= 5.30.3-4), po-debconf (= 1.0.21), procps (= 2:3.3.16-5), python3 (= 3.8.2-3), python3-dev (= 3.8.2-3), python3-distutils (= 3.8.5-1), python3-lib2to3 (= 3.8.5-1), python3-minimal (= 3.8.2-3), python3-pkg-resources (= 49.3.1-2), python3-setuptools (= 49.3.1-2), python3.8 (= 3.8.6-1), python3.8-dev (= 3.8.6-1), python3.8-minimal (= 3.8.6-1), readline-common (= 8.0-4), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), swig (= 4.0.1-5), swig4.0 (= 4.0.1-5), sysvinit-utils (= 2.96-5), tar (= 1.30+dfsg-7), util-linux (= 2.36-3+b1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C" LC_ALL="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1595496923" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ apbs-data_3.0.0+dfsg1-3_all.deb ------------------------------- new Debian package, version 2.0. size 226122852 bytes: control archive=13260 bytes. 706 bytes, 19 lines control 46928 bytes, 551 lines md5sums Package: apbs-data Source: apbs Version: 3.0.0+dfsg1-3 Architecture: all Maintainer: Debichem Team Installed-Size: 1182985 Breaks: apbs (<= 1.4-2) Section: science Priority: optional Multi-Arch: foreign Homepage: http://www.poissonboltzmann.org/ Description: data files for APBS (Adaptive Poisson Boltzmann Solver) APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains all data files for apbs package to reduce the redundancy between architectures in Debian. drwxr-xr-x root/root 0 2020-07-23 09:35 ./ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/examples/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/ -rw-r--r-- root/root 118791 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr -rw-r--r-- root/root 5354 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in -rw-r--r-- root/root 18579 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/1d7h-dmso-mol.out -rw-r--r-- root/root 5367 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in -rw-r--r-- root/root 18736 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/1d7h-dmso-smol.out drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/1d7h-dmso/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/ -rw-r--r-- root/root 103106 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd -rw-r--r-- root/root 13309 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp -rw-r--r-- root/root 183314 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log -rw-r--r-- root/root 183314 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog -rw-r--r-- root/root 628 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd -rwxr-xr-x root/root 181 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd -rw-r--r-- root/root 118073 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7h-min.pqr -rw-r--r-- root/root 119067 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr -rw-r--r-- root/root 5341 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7i-dss-mol.in -rw-r--r-- root/root 18569 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/1d7i-dss-mol.out -rw-r--r-- root/root 5353 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7i-dss-smol.in -rw-r--r-- root/root 18726 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/1d7i-dss-smol.out drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/1d7i-dss/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/ -rw-r--r-- root/root 103106 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd -rw-r--r-- root/root 13305 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp -rw-r--r-- root/root 183310 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.log -rw-r--r-- root/root 868 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd -rw-r--r-- root/root 118073 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/1d7i-min.pqr -rw-r--r-- root/root 4384 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/README.md -rw-r--r-- root/root 718 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/dmso-min.pqr -rw-r--r-- root/root 994 2020-05-30 01:47 ./usr/share/apbs/examples/FKBP/dss-min.pqr -rw-r--r-- root/root 312213 2020-07-23 09:35 ./usr/share/apbs/examples/FKBP/io.mc -rw-r--r-- root/root 4276 2020-05-30 01:47 ./usr/share/apbs/examples/README.md drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/examples/actin-dimer/ -rw-r--r-- root/root 5879 2020-05-30 01:47 ./usr/share/apbs/examples/actin-dimer/README.md drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/examples/actin-dimer/UHBD/ -rw-r--r-- root/root 27551 2020-05-30 01:47 ./usr/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat -rw-r--r-- root/root 24783 2020-05-30 01:47 ./usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.full.log -rw-r--r-- root/root 2156 2020-05-30 01:47 ./usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp -rw-r--r-- root/root 393759 2020-05-30 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12 lines control 1989 bytes, 19 lines md5sums Package: apbs-dbgsym Source: apbs Version: 3.0.0+dfsg1-3 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 311 Depends: apbs (= 3.0.0+dfsg1-3) Section: debug Priority: optional Description: debug symbols for apbs Build-Ids: 068f976707c612da1b9663da6c77e849e0381440 0980af42a1adebfe03eb76d6d1cdd7eab91cedc2 0aeba1822e4d4631911b840d0e337d0cd6604cfa 10a4abf0701c0eeaffb8b6b1a8d39b36ce7beb50 27e876a57b61beeb933ad91714569d859436bce0 41701b1e7dcc1dd2beed57686eb1e2cb999b7182 456a087dbb508ce602b47957a3596fbb90b9f8e0 4661d709d66c300e08f56e54f2563cb3942da862 4b61f0540dc49d6b403cef85d210424b9665127b 614b6f60357b56bc228976cb8113853df9f6dc0a 7faf92f814e0b2b5689054678b80b72f9109d597 9a33308a4077cf1ce8a25b32c2ea2fc5ee726043 9d366d1882905a8a612aaf92e54c3f141daaf614 a21cbaee94d09411b5db071ea522f6157c51451e b07b1bde64f9b447819aa05e2ef735744aeb8bd7 e69bad4595252cc76e736afe10718158d3adaa1b 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2020-07-23 09:35 ./usr/lib/debug/.dwz/x86_64-linux-gnu/apbs.debug drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-07-23 09:35 ./usr/share/doc/apbs-dbgsym -> apbs apbs_3.0.0+dfsg1-3_amd64.deb ---------------------------- new Debian package, version 2.0. size 86180 bytes: control archive=1724 bytes. 1424 bytes, 29 lines control 1686 bytes, 25 lines md5sums Package: apbs Version: 3.0.0+dfsg1-3 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 432 Depends: apbs-data (= 3.0.0+dfsg1-3), libapbs3 (= 3.0.0+dfsg1-3), libc6 (>= 2.29), libgomp1 (>= 4.2.1), libmaloc1 (>= 0.2-1), libopenmpi3 (>= 4.0.5), libstdc++6 (>= 4.1.1) Section: science Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. . This package contains the apbs program and utilities. drwxr-xr-x root/root 0 2020-07-23 09:35 ./ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/bin/ -rwxr-xr-x root/root 108688 2020-07-23 09:35 ./usr/bin/apbs drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/apbs/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/apbs/tools/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/ -rwxr-xr-x root/root 18576 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/analysis -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/benchmark -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/born -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/coulomb -rwxr-xr-x root/root 14488 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/del2dx -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/dx2mol -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/dx2uhbd -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/dxmath -rwxr-xr-x root/root 22672 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/mergedx -rwxr-xr-x root/root 26768 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/mergedx2 -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/mgmesh -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/multivalue -rwxr-xr-x root/root 26768 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/similarity -rwxr-xr-x root/root 18576 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/smooth -rwxr-xr-x root/root 14488 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/tensor2dx -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/uhbd_asc2bin -rwxr-xr-x root/root 14480 2020-07-23 09:35 ./usr/lib/apbs/tools/bin/bin/value drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/doc/apbs/ -rw-r--r-- root/root 78 2020-05-30 01:47 ./usr/share/doc/apbs/README -rw-r--r-- root/root 294 2020-07-23 09:35 ./usr/share/doc/apbs/README.test -rw-r--r-- root/root 805 2020-05-30 01:47 ./usr/share/doc/apbs/ReleaseNotes.md -rw-r--r-- root/root 5241 2020-07-23 09:35 ./usr/share/doc/apbs/changelog.Debian.gz -rw-r--r-- root/root 1453 2020-05-30 01:47 ./usr/share/doc/apbs/changelog.gz -rw-r--r-- root/root 3720 2020-07-23 09:35 ./usr/share/doc/apbs/copyright drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/man/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/man/man1/ -rw-r--r-- root/root 835 2020-07-23 09:35 ./usr/share/man/man1/apbs.1.gz libapbs-dev_3.0.0+dfsg1-3_amd64.deb ----------------------------------- new Debian package, version 2.0. size 66316 bytes: control archive=2000 bytes. 673 bytes, 19 lines control 3403 bytes, 51 lines md5sums Package: libapbs-dev Source: apbs Version: 3.0.0+dfsg1-3 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 579 Depends: libapbs3 (= 3.0.0+dfsg1-3) Section: libdevel Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the development headers to build against libapbs_* shared libraries. drwxr-xr-x root/root 0 2020-07-23 09:35 ./ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/include/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/include/apbs/ -rw-r--r-- root/root 3322 2020-05-30 01:47 ./usr/include/apbs/apbs.h drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/include/apbs/generic/ -rw-r--r-- root/root 8229 2020-05-30 01:47 ./usr/include/apbs/generic/apolparm.h -rw-r--r-- root/root 6401 2020-05-30 01:47 ./usr/include/apbs/generic/bemparm.h -rw-r--r-- root/root 8873 2020-05-30 01:47 ./usr/include/apbs/generic/femparm.h -rw-r--r-- root/root 6121 2020-05-30 01:47 ./usr/include/apbs/generic/geoflowparm.h -rw-r--r-- root/root 12602 2020-05-30 01:47 ./usr/include/apbs/generic/mgparm.h -rw-r--r-- root/root 21063 2020-05-30 01:47 ./usr/include/apbs/generic/nosh.h -rw-r--r-- root/root 10919 2020-05-30 01:47 ./usr/include/apbs/generic/pbamparm.h 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09:35 ./usr/share/doc/libapbs-dev/changelog.Debian.gz -rw-r--r-- root/root 1453 2020-05-30 01:47 ./usr/share/doc/libapbs-dev/changelog.gz -rw-r--r-- root/root 3720 2020-07-23 09:35 ./usr/share/doc/libapbs-dev/copyright libapbs3-dbgsym_3.0.0+dfsg1-3_amd64.deb --------------------------------------- new Debian package, version 2.0. size 548416 bytes: control archive=756 bytes. 504 bytes, 13 lines control 509 bytes, 5 lines md5sums Package: libapbs3-dbgsym Source: apbs Version: 3.0.0+dfsg1-3 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 600 Depends: libapbs3 (= 3.0.0+dfsg1-3) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libapbs3 Build-Ids: 2985a3cb69892b82e5901ec00aad97ef7704335b 940944169ca8bb47faaa7dd7d2e13ce91c99b97a c3a5d75b793422c00c6c53a5b9f373bb69240780 f0c163ef384a6c339632eebdb8156d2cdd7e26cf drwxr-xr-x root/root 0 2020-07-23 09:35 ./ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/ drwxr-xr-x 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Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the libapbs_* shared libraries. drwxr-xr-x root/root 0 2020-07-23 09:35 ./ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 223224 2020-07-23 09:35 ./usr/lib/x86_64-linux-gnu/libapbs_generic.so.3 -rw-r--r-- root/root 186360 2020-07-23 09:35 ./usr/lib/x86_64-linux-gnu/libapbs_mg.so.3 -rw-r--r-- root/root 239456 2020-07-23 09:35 ./usr/lib/x86_64-linux-gnu/libapbs_pmgc.so.3 -rw-r--r-- root/root 92152 2020-07-23 09:35 ./usr/lib/x86_64-linux-gnu/libapbs_routines.so.3 drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/doc/libapbs3/ -rw-r--r-- root/root 5241 2020-07-23 09:35 ./usr/share/doc/libapbs3/changelog.Debian.gz -rw-r--r-- root/root 3720 2020-07-23 09:35 ./usr/share/doc/libapbs3/copyright drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 95 2020-07-23 09:35 ./usr/share/lintian/overrides/libapbs3 python3-apbslib-dbgsym_3.0.0+dfsg1-3_amd64.deb ---------------------------------------------- new Debian package, version 2.0. size 158692 bytes: control archive=540 bytes. 385 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: python3-apbslib-dbgsym Source: apbs Version: 3.0.0+dfsg1-3 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 184 Depends: python3-apbslib (= 3.0.0+dfsg1-3) Section: debug Priority: optional Description: debug symbols for python3-apbslib Build-Ids: d8d5a9b0c5d4300e24f19a32abaeef78c18a2672 drwxr-xr-x root/root 0 2020-07-23 09:35 ./ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/debug/.build-id/d8/ -rw-r--r-- root/root 178000 2020-07-23 09:35 ./usr/lib/debug/.build-id/d8/d5a9b0c5d4300e24f19a32abaeef78c18a2672.debug drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-07-23 09:35 ./usr/share/doc/python3-apbslib-dbgsym -> python3-apbslib python3-apbslib_3.0.0+dfsg1-3_amd64.deb --------------------------------------- new Debian package, version 2.0. size 103932 bytes: control archive=1836 bytes. 779 bytes, 18 lines control 2086 bytes, 27 lines md5sums 255 bytes, 12 lines * postinst #!/bin/sh 404 bytes, 12 lines * prerm #!/bin/sh Package: python3-apbslib Source: apbs Version: 3.0.0+dfsg1-3 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 714 Depends: libapbs3 (= 3.0.0+dfsg1-3), python3 (<< 3.9), python3 (>= 3.8~), python3:any, libc6 (>= 2.14), libmaloc1 (>= 0.2-1), libpython3.8 (>= 3.8.2) Section: python Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package provides the apbslib module for Python3 enabling Python applications to access apbs. drwxr-xr-x root/root 0 2020-07-23 09:35 ./ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/python3/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/lib/python3/dist-packages/apbslib/ -rw-r--r-- root/root 23 2020-07-23 09:35 ./usr/lib/python3/dist-packages/apbslib/__init__.py -rw-r--r-- root/root 150848 2020-07-23 09:35 ./usr/lib/python3/dist-packages/apbslib/_apbslib.cpython-38-x86_64-linux-gnu.so -rw-r--r-- root/root 14632 2020-07-23 09:35 ./usr/lib/python3/dist-packages/apbslib/apbslib.py drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/tools/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/tools/python/ -rw-r--r-- root/root 1827 2020-05-30 01:47 ./usr/share/apbs/tools/python/CMakeLists.txt -rw-r--r-- root/root 20999 2020-05-30 01:47 ./usr/share/apbs/tools/python/Makefile -rw-r--r-- root/root 898 2020-05-30 01:47 ./usr/share/apbs/tools/python/Makefile.am -rw-r--r-- root/root 20457 2020-05-30 01:47 ./usr/share/apbs/tools/python/Makefile.in -rw-r--r-- root/root 1834 2020-05-30 01:47 ./usr/share/apbs/tools/python/README -rw-r--r-- root/root 6111 2020-05-30 01:47 ./usr/share/apbs/tools/python/apbs.in -rw-r--r-- root/root 260299 2020-05-30 01:47 ./usr/share/apbs/tools/python/apbslib.c -rw-r--r-- root/root 14676 2020-05-30 01:47 ./usr/share/apbs/tools/python/apbslib.i -rw-r--r-- root/root 11686 2020-05-30 01:47 ./usr/share/apbs/tools/python/apbslib_wrap.doc -rw-r--r-- root/root 66 2020-05-30 01:47 ./usr/share/apbs/tools/python/ion.pqr -rw-r--r-- root/root 14022 2020-05-30 01:47 ./usr/share/apbs/tools/python/main.py -rw-r--r-- root/root 17757 2020-07-23 09:35 ./usr/share/apbs/tools/python/noinput.py drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/apbs/tools/python/vgrid/ -rw-r--r-- root/root 15551 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/Makefile -rw-r--r-- root/root 845 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/Makefile.am -rw-r--r-- root/root 15036 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/Makefile.in -rw-r--r-- root/root 1638 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/README -rw-r--r-- root/root 2980 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/average.py -rw-r--r-- root/root 14037 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/mergedx.py -rw-r--r-- root/root 2255 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/read.py -rw-r--r-- root/root 3038 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/vgrid.i -rw-r--r-- root/root 4449 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/vgrid.py -rw-r--r-- root/root 97218 2020-05-30 01:47 ./usr/share/apbs/tools/python/vgrid/vgridlib.c drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-23 09:35 ./usr/share/doc/python3-apbslib/ -rw-r--r-- root/root 5241 2020-07-23 09:35 ./usr/share/doc/python3-apbslib/changelog.Debian.gz -rw-r--r-- root/root 3720 2020-07-23 09:35 ./usr/share/doc/python3-apbslib/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 3934932 Build-Time: 3347 Distribution: sid Host Architecture: amd64 Install-Time: 48 Job: /srv/debomatic/incoming/apbs_3.0.0+dfsg1-3.dsc Machine Architecture: amd64 Package: apbs Package-Time: 3411 Source-Version: 3.0.0+dfsg1-3 Space: 3934932 Status: successful Version: 3.0.0+dfsg1-3 -------------------------------------------------------------------------------- Finished at 2020-10-03T00:29:39Z Build needed 00:56:51, 3934932k disk space