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Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
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make doesn't install everything #31

Closed dvdesolve closed 2 years ago

dvdesolve commented 4 years ago

I'm trying to install apbs on Arch Linux following these steps:

git clone https://github.com/Electrostatics/apbs-pdb2pqr.git
cd apbs-pdb2pqr/
git submodule init
git submodule update
cd apbs
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ..
make
mkdir -p /tmp/dist
make DESTDIR=/tmp/dist install

However, it installs only the following files:

.:
total 0
drwxr-xr-x  3 viktor viktor  60 Feb 25 19:59 .
drwxrwxrwt 18 root   root   980 Feb 26 17:27 ..
drwxr-xr-x  6 viktor viktor 120 Feb 25 19:59 usr

./usr:
total 0
drwxr-xr-x 6 viktor viktor 120 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor  60 Feb 25 19:59 bin
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 include
drwxr-xr-x 2 viktor viktor 140 Feb 25 19:59 lib
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 share

./usr/bin:
total 276K
drwxr-xr-x 2 viktor viktor   60 Feb 25 19:59 .
drwxr-xr-x 6 viktor viktor  120 Feb 25 19:59 ..
-rwxr-xr-x 1 viktor viktor 274K Feb 25 19:58 apbs

./usr/include:
total 0
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 .
drwxr-xr-x 6 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x 5 viktor viktor 140 Feb 25 19:59 apbs
drwxr-xr-x 2 viktor viktor 300 Feb 25 19:59 maloc

./usr/include/apbs:
total 40K
drwxr-xr-x 5 viktor viktor  140 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 3.3K Feb 25 17:50 apbs.h
drwxr-xr-x 2 viktor viktor  460 Feb 25 19:59 generic
drwxr-xr-x 2 viktor viktor  140 Feb 25 19:59 mg
drwxr-xr-x 2 viktor viktor  400 Feb 25 19:59 pmgc
-rw-r--r-- 1 viktor viktor  33K Feb 25 17:50 routines.h

./usr/include/apbs/generic:
total 288K
drwxr-xr-x 2 viktor viktor  460 Feb 25 19:59 .
drwxr-xr-x 5 viktor viktor  140 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 8.1K Feb 25 17:50 apolparm.h
-rw-r--r-- 1 viktor viktor 6.3K Feb 25 17:50 bemparm.h
-rw-r--r-- 1 viktor viktor 8.7K Feb 25 17:50 femparm.h
-rw-r--r-- 1 viktor viktor 6.0K Feb 25 17:50 geoflowparm.h
-rw-r--r-- 1 viktor viktor  13K Feb 25 17:50 mgparm.h
-rw-r--r-- 1 viktor viktor  21K Feb 25 17:50 nosh.h
-rw-r--r-- 1 viktor viktor  11K Feb 25 17:50 pbamparm.h
-rw-r--r-- 1 viktor viktor  11K Feb 25 17:50 pbeparm.h
-rw-r--r-- 1 viktor viktor 7.5K Feb 25 17:50 pbsamparm.h
-rw-r--r-- 1 viktor viktor  23K Feb 25 17:50 vacc.h
-rw-r--r-- 1 viktor viktor 8.3K Feb 25 17:50 valist.h
-rw-r--r-- 1 viktor viktor  13K Feb 25 17:50 vatom.h
-rw-r--r-- 1 viktor viktor 5.9K Feb 25 17:50 vcap.h
-rw-r--r-- 1 viktor viktor 9.1K Feb 25 17:50 vclist.h
-rw-r--r-- 1 viktor viktor  13K Feb 25 17:50 vgreen.h
-rw-r--r-- 1 viktor viktor  38K Feb 25 17:50 vhal.h
-rw-r--r-- 1 viktor viktor 3.1K Feb 25 17:50 vmatrix.h
-rw-r--r-- 1 viktor viktor  12K Feb 25 17:50 vparam.h
-rw-r--r-- 1 viktor viktor  20K Feb 25 17:50 vpbe.h
-rw-r--r-- 1 viktor viktor 5.1K Feb 25 17:50 vstring.h
-rw-r--r-- 1 viktor viktor 3.9K Feb 25 17:50 vunit.h

./usr/include/apbs/mg:
total 100K
drwxr-xr-x 2 viktor viktor  140 Feb 25 19:59 .
drwxr-xr-x 5 viktor viktor  140 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  15K Feb 25 17:50 vgrid.h
-rw-r--r-- 1 viktor viktor 6.8K Feb 25 17:50 vmgrid.h
-rw-r--r-- 1 viktor viktor 6.1K Feb 25 17:50 vopot.h
-rw-r--r-- 1 viktor viktor  53K Feb 25 17:50 vpmg.h
-rw-r--r-- 1 viktor viktor  11K Feb 25 17:50 vpmgp.h

./usr/include/apbs/pmgc:
total 192K
drwxr-xr-x 2 viktor viktor  400 Feb 25 19:59 .
drwxr-xr-x 5 viktor viktor  140 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  13K Feb 25 17:50 buildAd.h
-rw-r--r-- 1 viktor viktor 5.2K Feb 25 17:50 buildBd.h
-rw-r--r-- 1 viktor viktor  17K Feb 25 17:50 buildGd.h
-rw-r--r-- 1 viktor viktor 9.9K Feb 25 17:50 buildPd.h
-rw-r--r-- 1 viktor viktor 3.4K Feb 25 17:50 cgd.h
-rw-r--r-- 1 viktor viktor 5.7K Feb 25 17:50 gsd.h
-rw-r--r-- 1 viktor viktor  19K Feb 25 17:50 matvecd.h
-rw-r--r-- 1 viktor viktor 5.7K Feb 25 17:50 mgcsd.h
-rw-r--r-- 1 viktor viktor 9.1K Feb 25 17:50 mgdrvd.h
-rw-r--r-- 1 viktor viktor 7.6K Feb 25 17:50 mgfasd.h
-rw-r--r-- 1 viktor viktor  15K Feb 25 17:50 mgsubd.h
-rw-r--r-- 1 viktor viktor  12K Feb 25 17:50 mikpckd.h
-rw-r--r-- 1 viktor viktor 4.0K Feb 25 17:50 mlinpckd.h
-rw-r--r-- 1 viktor viktor 7.6K Feb 25 17:50 mypdec.h
-rw-r--r-- 1 viktor viktor 5.9K Feb 25 17:50 newdrvd.h
-rw-r--r-- 1 viktor viktor 6.6K Feb 25 17:50 newtond.h
-rw-r--r-- 1 viktor viktor 8.1K Feb 25 17:50 powerd.h
-rw-r--r-- 1 viktor viktor 4.6K Feb 25 17:50 smoothd.h

./usr/include/maloc:
total 140K
drwxr-xr-x 2 viktor viktor  300 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  12K Feb 25 17:52 maloc_base.h
-rw-r--r-- 1 viktor viktor 1.4K Feb 25 17:52 maloc.h
-rw-r--r-- 1 viktor viktor 1.8K Feb 25 17:52 psh.h
-rw-r--r-- 1 viktor viktor 9.4K Feb 25 17:52 vcom.h
-rw-r--r-- 1 viktor viktor  14K Feb 25 17:52 vio.h
-rw-r--r-- 1 viktor viktor 8.2K Feb 25 17:52 vmem.h
-rw-r--r-- 1 viktor viktor 4.9K Feb 25 17:52 vmp.h
-rw-r--r-- 1 viktor viktor 6.2K Feb 25 17:52 vmpi.h
-rw-r--r-- 1 viktor viktor  19K Feb 25 17:52 vnm.h
-rw-r--r-- 1 viktor viktor  12K Feb 25 17:52 vpred.h
-rw-r--r-- 1 viktor viktor  14K Feb 25 17:52 vset.h
-rw-r--r-- 1 viktor viktor 9.4K Feb 25 17:52 vsh.h
-rw-r--r-- 1 viktor viktor 1.4K Feb 25 17:52 vsys.h

./usr/lib:
total 4.6M
drwxr-xr-x 2 viktor viktor  140 Feb 25 19:59 .
drwxr-xr-x 6 viktor viktor  120 Feb 25 19:59 ..
-rwxr-xr-x 1 viktor viktor 717K Feb 25 19:58 libapbs_generic.so
-rwxr-xr-x 1 viktor viktor 602K Feb 25 19:58 libapbs_mg.so
-rwxr-xr-x 1 viktor viktor 927K Feb 25 19:58 libapbs_pmgc.so
-rwxr-xr-x 1 viktor viktor 235K Feb 25 19:58 libapbs_routines.so
-rwxr-xr-x 1 viktor viktor 2.2M Feb 25 19:58 libmaloc.so

./usr/share:
total 0
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 6 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x 6 viktor viktor 120 Feb 25 19:59 apbs

./usr/share/apbs:
total 0
drwxr-xr-x  6 viktor viktor 120 Feb 25 19:59 .
drwxr-xr-x  3 viktor viktor  60 Feb 25 19:59 ..
drwxr-xr-x  5 viktor viktor 180 Feb 25 19:59 doc
drwxr-xr-x 26 viktor viktor 540 Feb 25 19:59 examples
drwxr-xr-x  2 viktor viktor 140 Feb 25 19:59 tests
drwxr-xr-x 12 viktor viktor 260 Feb 25 19:59 tools

./usr/share/apbs/doc:
total 16K
drwxr-xr-x 5 viktor viktor  180 Feb 25 19:59 .
drwxr-xr-x 6 viktor viktor  120 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 2.6K Feb 25 17:50 ChangeLog.md
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 data-ontology
drwxr-xr-x 2 viktor viktor  200 Feb 25 19:59 icons
drwxr-xr-x 2 viktor viktor   80 Feb 25 19:59 license
-rw-r--r-- 1 viktor viktor  270 Feb 25 17:50 README
-rw-r--r-- 1 viktor viktor  805 Feb 25 17:50 ReleaseNotes.md
-rw-r--r-- 1 viktor viktor 3.7K Feb 25 17:50 release_procedure.txt

./usr/share/apbs/doc/data-ontology:
total 36K
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 .
drwxr-xr-x 5 viktor viktor 180 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 265 Feb 25 17:50 catalog-v001.xml
-rw-r--r-- 1 viktor viktor 23K Feb 25 17:50 data-ontology.ttl
-rw-r--r-- 1 viktor viktor 560 Feb 25 17:50 protege.sh
-rw-r--r-- 1 viktor viktor  85 Feb 25 17:50 README.md

./usr/share/apbs/doc/icons:
total 324K
drwxr-xr-x 2 viktor viktor  200 Feb 25 19:59 .
drwxr-xr-x 5 viktor viktor  180 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 167K Feb 25 17:50 APBS_1024.png
-rw-r--r-- 1 viktor viktor  16K Feb 25 17:50 APBS_128.png
-rw-r--r-- 1 viktor viktor 6.4K Feb 25 17:50 APBS_128_v2.png
-rw-r--r-- 1 viktor viktor  710 Feb 25 17:50 APBS_16.png
-rw-r--r-- 1 viktor viktor  37K Feb 25 17:50 APBS_256.png
-rw-r--r-- 1 viktor viktor 1.5K Feb 25 17:50 APBS_32.png
-rw-r--r-- 1 viktor viktor  78K Feb 25 17:50 APBS_512.png
-rw-r--r-- 1 viktor viktor 3.0K Feb 25 17:50 APBS_64.png

./usr/share/apbs/doc/license:
total 8.0K
drwxr-xr-x 2 viktor viktor   80 Feb 25 19:59 .
drwxr-xr-x 5 viktor viktor  180 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 2.5K Feb 25 17:50 license.html
-rw-r--r-- 1 viktor viktor 2.1K Feb 25 17:50 LICENSE.txt

./usr/share/apbs/examples:
total 8.0K
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 .
drwxr-xr-x  6 viktor viktor  120 Feb 25 19:59 ..
drwxr-xr-x  3 viktor viktor  240 Feb 25 19:59 actin-dimer
drwxr-xr-x  2 viktor viktor  400 Feb 25 19:59 alkanes
drwxr-xr-x  3 viktor viktor  180 Feb 25 19:59 bem
drwxr-xr-x  3 viktor viktor  140 Feb 25 19:59 bem-binding-energy
drwxr-xr-x  3 viktor viktor  200 Feb 25 19:59 bem-pKa
drwxr-xr-x  2 viktor viktor  380 Feb 25 19:59 born
drwxr-xr-x  4 viktor viktor  300 Feb 25 19:59 FKBP
drwxr-xr-x  2 viktor viktor  200 Feb 25 19:59 geoflow
drwxr-xr-x  3 viktor viktor  200 Feb 25 19:59 hca-bind
drwxr-xr-x  2 viktor viktor  240 Feb 25 19:59 helix
drwxr-xr-x  3 viktor viktor  240 Feb 25 19:59 ionize
drwxr-xr-x  2 viktor viktor  200 Feb 25 19:59 ion-pmf
drwxr-xr-x  3 viktor viktor  220 Feb 25 19:59 ion-protein
drwxr-xr-x  2 viktor viktor  100 Feb 25 19:59 membrane
drwxr-xr-x  2 viktor viktor  180 Feb 25 19:59 misc
drwxr-xr-x  2 viktor viktor  180 Feb 25 19:59 opal
drwxr-xr-x  2 viktor viktor  320 Feb 25 19:59 pbam
drwxr-xr-x  2 viktor viktor  100 Feb 25 19:59 pbsam-barn_bars
drwxr-xr-x  3 viktor viktor  300 Feb 25 19:59 pbsam-gly
drwxr-xr-x  3 viktor viktor  220 Feb 25 19:59 pka-lig
drwxr-xr-x  2 viktor viktor  400 Feb 25 19:59 point-pmf
drwxr-xr-x  3 viktor viktor  340 Feb 25 19:59 protein-rna
-rw-r--r--  1 viktor viktor 4.2K Feb 25 17:50 README.md
drwxr-xr-x  2 viktor viktor  140 Feb 25 19:59 smpbe
drwxr-xr-x  3 viktor viktor  200 Feb 25 19:59 solv

./usr/share/apbs/examples/actin-dimer:
total 1.6M
drwxr-xr-x  3 viktor viktor  240 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 apbs-mol-auto.in
-rw-r--r--  1 viktor viktor 1.9K Feb 25 17:50 apbs-mol-parallel.in
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 apbs-smol-auto.in
-rw-r--r--  1 viktor viktor 1.9K Feb 25 17:50 apbs-smol-parallel.in
-rw-r--r--  1 viktor viktor 781K Feb 25 17:50 complex.pqr
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 mesh.m
-rw-r--r--  1 viktor viktor 391K Feb 25 17:50 mol1.pqr
-rw-r--r--  1 viktor viktor 391K Feb 25 17:50 mol2.pqr
-rw-r--r--  1 viktor viktor 5.6K Feb 25 17:50 README.md
drwxr-xr-x  2 viktor viktor  180 Feb 25 19:59 UHBD

./usr/share/apbs/examples/actin-dimer/UHBD:
total 2.8M
drwxr-xr-x 2 viktor viktor  180 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  240 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  27K Feb 25 17:50 aheall-atom.charmm.dat
-rw-r--r-- 1 viktor viktor  25K Feb 25 17:50 nuc.3-4.full.log
-rw-r--r-- 1 viktor viktor 2.2K Feb 25 17:50 nuc.3-4.inp
-rw-r--r-- 1 viktor viktor 385K Feb 25 17:50 prot3.pdb
-rw-r--r-- 1 viktor viktor 385K Feb 25 17:50 prot4.pdb
-rw-r--r-- 1 viktor viktor  920 Feb 25 17:50 single.inp
-rw-r--r-- 1 viktor viktor 1.9M Feb 25 17:50 srsrf.dot

./usr/share/apbs/examples/alkanes:
total 92K
drwxr-xr-x  2 viktor viktor  400 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 1.2K Feb 25 17:50 2-methylbutane.pdb
-rw-r--r--  1 viktor viktor 3.0K Feb 25 17:50 alkanes.in
-rw-r--r--  1 viktor viktor  285 Feb 25 17:50 apbs-forces.in
-rw-r--r--  1 viktor viktor 1019 Feb 25 17:50 butane.pdb
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 cyclohexane.pdb
-rw-r--r--  1 viktor viktor  894 Feb 25 17:50 cyclopentane.pdb
-rw-r--r--  1 viktor viktor  553 Feb 25 17:50 ethane.pdb
-rw-r--r--  1 viktor viktor 5.2K Feb 25 17:50 force.result
-rw-r--r--  1 viktor viktor 1.4K Feb 25 17:50 hexane.pdb
-rw-r--r--  1 viktor viktor 1007 Feb 25 17:50 isobutane.pdb
-rw-r--r--  1 viktor viktor  11K Feb 25 17:50 Makefile.in
-rw-r--r--  1 viktor viktor  355 Feb 25 17:50 methane.pdb
-rw-r--r--  1 viktor viktor  781 Feb 25 17:50 mol.pdb
-rw-r--r--  1 viktor viktor 1.2K Feb 25 17:50 neopentane.pdb
-rw-r--r--  1 viktor viktor  620 Feb 25 17:50 parm.dat
-rw-r--r--  1 viktor viktor 1.2K Feb 25 17:50 pentane.pdb
-rw-r--r--  1 viktor viktor  781 Feb 25 17:50 propane.pdb
-rw-r--r--  1 viktor viktor  12K Feb 25 17:50 README.md

./usr/share/apbs/examples/bem:
total 24K
drwxr-xr-x  3 viktor viktor  180 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  885 Feb 25 17:50 1a63_msms.in
-rw-r--r--  1 viktor viktor  894 Feb 25 17:50 1a63_NanoShaper_SES.in
-rw-r--r--  1 viktor viktor  885 Feb 25 17:50 1a63_NanoShaper_Skin.in
-rw-r--r--  1 viktor viktor  884 Feb 25 17:50 451c_order1.in
-rw-r--r--  1 viktor viktor  884 Feb 25 17:50 451c_order5.in
-rw-r--r--  1 viktor viktor 1.5K Feb 25 17:50 README.md
drwxr-xr-x  2 viktor viktor  180 Feb 25 19:59 test_proteins

./usr/share/apbs/examples/bem/test_proteins:
total 336K
drwxr-xr-x 2 viktor viktor  180 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  180 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 151K Feb 25 17:50 1a63.pqr
-rw-r--r-- 1 viktor viktor  38K Feb 25 17:50 1ajj.pqr
-rw-r--r-- 1 viktor viktor  42K Feb 25 17:50 1bbl.pqr
-rw-r--r-- 1 viktor viktor  88K Feb 25 17:50 451c.pqr
-rw-r--r-- 1 viktor viktor   40 Feb 25 17:50 oneb.pqr
-rw-r--r-- 1 viktor viktor   82 Feb 25 17:50 twob2.pqr
-rw-r--r-- 1 viktor viktor   80 Feb 25 17:50 twob.pqr

./usr/share/apbs/examples/bem-binding-energy:
total 16K
drwxr-xr-x  3 viktor viktor  140 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  885 Feb 25 17:50 1d30.in
-rw-r--r--  1 viktor viktor  894 Feb 25 17:50 1d30_monomer1.in
-rw-r--r--  1 viktor viktor  895 Feb 25 17:50 1d30_monomer2.in
-rw-r--r--  1 viktor viktor 1014 Feb 25 17:50 README.md
drwxr-xr-x  2 viktor viktor  100 Feb 25 19:59 test_proteins

./usr/share/apbs/examples/bem-binding-energy/test_proteins:
total 92K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  140 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  41K Feb 25 17:50 1d30_monomer1.pqr
-rw-r--r-- 1 viktor viktor 2.1K Feb 25 17:50 1d30_monomer2.pqr
-rw-r--r-- 1 viktor viktor  43K Feb 25 17:50 1d30.pqr

./usr/share/apbs/examples/bem-pKa:
total 28K
drwxr-xr-x  3 viktor viktor  200 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  893 Feb 25 17:50 2LZT-ASH66.in
-rw-r--r--  1 viktor viktor  893 Feb 25 17:50 2LZT-ASP66.in
-rw-r--r--  1 viktor viktor  895 Feb 25 17:50 2LZT-noASH66.in
-rw-r--r--  1 viktor viktor  895 Feb 25 17:50 2LZT-noASP66.in
-rw-r--r--  1 viktor viktor  873 Feb 25 17:50 ASH66.in
-rw-r--r--  1 viktor viktor  873 Feb 25 17:50 ASP66.in
-rw-r--r--  1 viktor viktor 1.1K Feb 25 17:50 README.md
drwxr-xr-x  2 viktor viktor  160 Feb 25 19:59 test_proteins

./usr/share/apbs/examples/bem-pKa/test_proteins:
total 552K
drwxr-xr-x 2 viktor viktor  160 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  200 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 135K Feb 25 17:50 2LZT-ASH66.pqr
-rw-r--r-- 1 viktor viktor 134K Feb 25 17:50 2LZT-ASP66.pqr
-rw-r--r-- 1 viktor viktor 135K Feb 25 17:50 2LZT-noASH66.pqr
-rw-r--r-- 1 viktor viktor 135K Feb 25 17:50 2LZT-noASP66.pqr
-rw-r--r-- 1 viktor viktor  910 Feb 25 17:50 ASH66.pqr
-rw-r--r-- 1 viktor viktor  840 Feb 25 17:50 ASP66.pqr

./usr/share/apbs/examples/born:
total 72K
drwxr-xr-x  2 viktor viktor  380 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  874 Feb 25 17:50 apbs-apolar.in
-rw-r--r--  1 viktor viktor 1.6K Feb 25 17:50 apbs-forces.in
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 apbs-mol-auto.in
-rw-r--r--  1 viktor viktor 1.2K Feb 25 17:50 apbs-mol-fem-extmesh.in
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 apbs-mol-fem.in
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 apbs-mol-parallel.in
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 apbs-smol-auto.in
-rw-r--r--  1 viktor viktor  779 Feb 25 17:50 apbs-smol-fem.in
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 apbs-smol-parallel.in
-rw-r--r--  1 viktor viktor  350 Feb 25 17:50 apolarforces
-rw-r--r--  1 viktor viktor   66 Feb 25 17:50 ion.pqr
-rw-r--r--  1 viktor viktor  388 Feb 25 17:50 ion.xml
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 mesh.m
-rw-r--r--  1 viktor viktor  524 Feb 25 17:50 parm.dat
-rw-r--r--  1 viktor viktor  643 Feb 25 17:50 pmf.dat
-rw-r--r--  1 viktor viktor  266 Feb 25 17:50 polarforces
-rw-r--r--  1 viktor viktor 4.4K Feb 25 17:50 README.md

./usr/share/apbs/examples/FKBP:
total 520K
drwxr-xr-x  4 viktor viktor  300 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
drwxr-xr-x  3 viktor viktor   60 Feb 25 19:59 1d7h-dmso
-rw-r--r--  1 viktor viktor 117K Feb 25 17:50 1d7h-dmso-complex.pqr
-rw-r--r--  1 viktor viktor 5.3K Feb 25 17:50 1d7h-dmso-mol.in
-rw-r--r--  1 viktor viktor 5.3K Feb 25 17:50 1d7h-dmso-smol.in
-rw-r--r--  1 viktor viktor 116K Feb 25 17:50 1d7h-min.pqr
drwxr-xr-x  3 viktor viktor   60 Feb 25 19:59 1d7i-dss
-rw-r--r--  1 viktor viktor 117K Feb 25 17:50 1d7i-dss-complex.pqr
-rw-r--r--  1 viktor viktor 5.3K Feb 25 17:50 1d7i-dss-mol.in
-rw-r--r--  1 viktor viktor 5.3K Feb 25 17:50 1d7i-dss-smol.in
-rw-r--r--  1 viktor viktor 116K Feb 25 17:50 1d7i-min.pqr
-rw-r--r--  1 viktor viktor  718 Feb 25 17:50 dmso-min.pqr
-rw-r--r--  1 viktor viktor  994 Feb 25 17:50 dss-min.pqr
-rw-r--r--  1 viktor viktor 4.3K Feb 25 17:50 README.md

./usr/share/apbs/examples/FKBP/1d7h-dmso:
total 0
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 300 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 160 Feb 25 19:59 UHBD

./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD:
total 488K
drwxr-xr-x 2 viktor viktor  160 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor   60 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 101K Feb 25 17:50 1d7h-min.qcd
-rw-r--r-- 1 viktor viktor  13K Feb 25 17:50 bindf.inp
-rw-r--r-- 1 viktor viktor 180K Feb 25 17:50 bindf.log
-rw-r--r-- 1 viktor viktor 180K Feb 25 17:50 bindf.oldlog
-rw-r--r-- 1 viktor viktor  628 Feb 25 17:50 dmso-min.qcd
-rw-r--r-- 1 viktor viktor  181 Feb 25 17:50 pqr2qcd

./usr/share/apbs/examples/FKBP/1d7i-dss:
total 0
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 300 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 UHBD

./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD:
total 304K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor   60 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 101K Feb 25 17:50 1d7i-min.qcd
-rw-r--r-- 1 viktor viktor  13K Feb 25 17:50 bindf.inp
-rw-r--r-- 1 viktor viktor 180K Feb 25 17:50 bindf.log
-rw-r--r-- 1 viktor viktor  868 Feb 25 17:50 dss-min.qcd

./usr/share/apbs/examples/geoflow:
total 180K
drwxr-xr-x  2 viktor viktor  200 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  686 Feb 25 17:50 1a63.in
-rw-r--r--  1 viktor viktor 151K Feb 25 17:50 1a63.pqr
-rw-r--r--  1 viktor viktor  668 Feb 25 17:50 glycerol.in
-rw-r--r--  1 viktor viktor  910 Feb 25 17:50 gly.pdb
-rw-r--r--  1 viktor viktor 1.5K Feb 25 17:50 gly.pqr
-rw-r--r--  1 viktor viktor  695 Feb 25 17:50 imidazole.in
-rw-r--r--  1 viktor viktor  532 Feb 25 17:50 imidazole_zap.pqr
-rw-r--r--  1 viktor viktor 1.1K Feb 25 17:50 README.md

./usr/share/apbs/examples/hca-bind:
total 352K
drwxr-xr-x  3 viktor viktor  200 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 1.2K Feb 25 17:50 acet.pqr
-rw-r--r--  1 viktor viktor 1.9K Feb 25 17:50 apbs-mol.in
-rw-r--r--  1 viktor viktor 1.9K Feb 25 17:50 apbs-smol.in
-rw-r--r--  1 viktor viktor 165K Feb 25 17:50 complex.pqr
-rw-r--r--  1 viktor viktor 164K Feb 25 17:50 hca.pqr
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 mesh.m
-rw-r--r--  1 viktor viktor 3.4K Feb 25 17:50 README.md
drwxr-xr-x  2 viktor viktor  240 Feb 25 19:59 UHBD

./usr/share/apbs/examples/hca-bind/UHBD:
total 1.6M
drwxr-xr-x 2 viktor viktor  240 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  200 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 151K Feb 25 17:50 bindf1.qcd
-rw-r--r-- 1 viktor viktor    0 Feb 25 17:50 bindf2.err
-rw-r--r-- 1 viktor viktor 1.1K Feb 25 17:50 bindf2.qcd
-rw-r--r-- 1 viktor viktor  14K Feb 25 17:50 bindf.inp
-rw-r--r-- 1 viktor viktor 250K Feb 25 17:50 bindf.log
-rw-r--r-- 1 viktor viktor    0 Feb 25 17:50 bindf-nmap.err
-rw-r--r-- 1 viktor viktor  14K Feb 25 17:50 bindf-nmap.inp
-rw-r--r-- 1 viktor viktor 255K Feb 25 17:50 bindf-nmap.out
-rw-r--r-- 1 viktor viktor 236K Feb 25 17:50 bindf.out.orig
-rw-r--r-- 1 viktor viktor 626K Feb 25 17:50 srsrf.dot

./usr/share/apbs/examples/helix:
total 164K
drwxr-xr-x  2 viktor viktor  240 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 2.4K Feb 25 17:50 Apbs_dummy.in
-rw-r--r--  1 viktor viktor 2.4K Feb 25 17:50 Apbs_dummy-TEMPLATE.in
-rw-r--r--  1 viktor viktor 3.4K Feb 25 17:50 Apbs_solv-TEMPLATE.in
-rw-r--r--  1 viktor viktor  25K Feb 25 17:50 draw_membrane2.c
-rw-r--r--  1 viktor viktor  23K Feb 25 17:50 Membrane-helix-0.pqr
-rw-r--r--  1 viktor viktor  23K Feb 25 17:50 Membrane-helix-12.pqr
-rw-r--r--  1 viktor viktor  23K Feb 25 17:50 Membrane-helix-16.pqr
-rw-r--r--  1 viktor viktor  23K Feb 25 17:50 Membrane-helix-4.pqr
-rw-r--r--  1 viktor viktor  23K Feb 25 17:50 Membrane-helix-8.pqr
-rw-r--r--  1 viktor viktor 3.1K Feb 25 17:50 Run_membrane-helix.sh

./usr/share/apbs/examples/ionize:
total 36K
drwxr-xr-x  3 viktor viktor  240 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  552 Feb 25 17:50 acetate.pqr
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 acetate.xml
-rw-r--r--  1 viktor viktor  552 Feb 25 17:50 acetic-acid.pqr
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 acetic-acid.xml
-rw-r--r--  1 viktor viktor 3.1K Feb 25 17:50 apbs-mol.in
-rw-r--r--  1 viktor viktor 3.1K Feb 25 17:50 apbs-smol.in
-rw-r--r--  1 viktor viktor   69 Feb 25 17:50 proton.pqr
-rw-r--r--  1 viktor viktor  354 Feb 25 17:50 proton.xml
-rw-r--r--  1 viktor viktor 2.9K Feb 25 17:50 README.md
drwxr-xr-x  2 viktor viktor  120 Feb 25 19:59 UHBD

./usr/share/apbs/examples/ionize/UHBD:
total 68K
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor 240 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 923 Feb 25 17:50 elec.dat.exam
-rw-r--r-- 1 viktor viktor 13K Feb 25 17:50 elec.inp.exam
-rw-r--r-- 1 viktor viktor 41K Feb 25 17:50 elec.out.orig.exam
-rw-r--r-- 1 viktor viktor 540 Feb 25 17:50 elec.pdb.exam

./usr/share/apbs/examples/ion-pmf:
total 52K
drwxr-xr-x  2 viktor viktor  200 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  642 Feb 25 17:50 apolarforces
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 complex.in
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 ion-pmf.in
-rw-r--r--  1 viktor viktor  136 Feb 25 17:50 ion-pmf.pdb
-rw-r--r--  1 viktor viktor  526 Feb 25 17:50 parm.dat
-rw-r--r--  1 viktor viktor  616 Feb 25 17:50 polarforces
-rw-r--r--  1 viktor viktor  24K Feb 25 17:50 README.md
-rw-r--r--  1 viktor viktor  910 Feb 25 17:50 runme.sh

./usr/share/apbs/examples/ion-protein:
total 64K
drwxr-xr-x  3 viktor viktor  220 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor   67 Feb 25 17:50 491.pqr
-rw-r--r--  1 viktor viktor 1.6K Feb 25 17:50 apbs-mol-pdiel12.in
-rw-r--r--  1 viktor viktor 1.6K Feb 25 17:50 apbs-mol-pdiel2.in
-rw-r--r--  1 viktor viktor 1.6K Feb 25 17:50 apbs-smol-pdiel12.in
-rw-r--r--  1 viktor viktor 1.6K Feb 25 17:50 apbs-smol-pdiel2.in
-rw-r--r--  1 viktor viktor  18K Feb 25 17:50 complex.pqr
-rw-r--r--  1 viktor viktor 3.2K Feb 25 17:50 README.md
-rw-r--r--  1 viktor viktor  18K Feb 25 17:50 small491.pqr
drwxr-xr-x  2 viktor viktor  140 Feb 25 19:59 UHBD

./usr/share/apbs/examples/ion-protein/UHBD:
total 84K
drwxr-xr-x 2 viktor viktor  140 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  220 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor   67 Feb 25 17:50 491.pdb
-rw-r--r-- 1 viktor viktor  25K Feb 25 17:50 small491.e2.log
-rw-r--r-- 1 viktor viktor 2.3K Feb 25 17:50 small491.inp
-rw-r--r-- 1 viktor viktor  25K Feb 25 17:50 small491.log
-rw-r--r-- 1 viktor viktor  17K Feb 25 17:50 small491.pdb

./usr/share/apbs/examples/membrane:
total 12K
drwxr-xr-x  2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  325 Feb 25 17:50 memv.in
-rw-r--r--  1 viktor viktor   70 Feb 25 17:50 pot.pqr
-rw-r--r--  1 viktor viktor 1.2K Feb 25 17:50 readme.md

./usr/share/apbs/examples/misc:
total 1.8M
drwxr-xr-x  2 viktor viktor  180 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 1.1M Feb 25 17:50 achbp.pqr
-rw-r--r--  1 viktor viktor  861 Feb 25 17:50 apbs.in
-rw-r--r--  1 viktor viktor  899 Feb 25 17:50 apbs-PDB.in
-rw-r--r--  1 viktor viktor  61K Feb 25 17:50 fas2.pqr
-rw-r--r--  1 viktor viktor 550K Feb 25 17:50 mache.pqr
-rw-r--r--  1 viktor viktor  68K Feb 25 17:50 param.dat
-rw-r--r--  1 viktor viktor  500 Feb 25 17:50 README.md

./usr/share/apbs/examples/opal:
total 1.6M
drwxr-xr-x  2 viktor viktor  180 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 781K Feb 25 17:50 actin-complex.pqr
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 actin-dimer.in
-rw-r--r--  1 viktor viktor 1.9K Feb 25 17:50 actin-dimer-para.in
-rw-r--r--  1 viktor viktor 391K Feb 25 17:50 actin-mol1.pqr
-rw-r--r--  1 viktor viktor 391K Feb 25 17:50 actin-mol2.pqr
-rw-r--r--  1 viktor viktor  388 Feb 25 17:50 born.xml
-rw-r--r--  1 viktor viktor 8.9K Feb 25 17:50 README.md

./usr/share/apbs/examples/pbam:
total 204K
drwxr-xr-x  2 viktor viktor  320 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  732 Feb 25 17:50 1a63.in
-rw-r--r--  1 viktor viktor 151K Feb 25 17:50 1a63.pqr
-rw-r--r--  1 viktor viktor   13 Feb 25 17:50 neg_1.xyz
-rw-r--r--  1 viktor viktor   13 Feb 25 17:50 neg_2.xyz
-rw-r--r--  1 viktor viktor   13 Feb 25 17:50 neg_3.xyz
-rw-r--r--  1 viktor viktor  210 Feb 25 17:50 neg_charge.pqr
-rw-r--r--  1 viktor viktor   15 Feb 25 17:50 pos_1.xyz
-rw-r--r--  1 viktor viktor   14 Feb 25 17:50 pos_2.xyz
-rw-r--r--  1 viktor viktor   13 Feb 25 17:50 pos_3.xyz
-rw-r--r--  1 viktor viktor  210 Feb 25 17:50 pos_charge.pqr
-rw-r--r--  1 viktor viktor 1015 Feb 25 17:50 README.md
-rw-r--r--  1 viktor viktor  933 Feb 25 17:50 toy_dynamics.in
-rw-r--r--  1 viktor viktor  739 Feb 25 17:50 toy_electrostatic.in
-rw-r--r--  1 viktor viktor  665 Feb 25 17:50 toy_energyforce.in

./usr/share/apbs/examples/pbsam-barn_bars:
total 236K
drwxr-xr-x  2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 126K Feb 25 17:50 barnase.pqr
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 barn_bars_electro.in
-rw-r--r--  1 viktor viktor 102K Feb 25 17:50 barstar.pqr

./usr/share/apbs/examples/pbsam-gly:
total 96K
drwxr-xr-x  3 viktor viktor  300 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 2.4K Feb 25 17:50 gly_cg2.pqr
-rw-r--r--  1 viktor viktor 2.4K Feb 25 17:50 gly_cg.pqr
-rw-r--r--  1 viktor viktor  975 Feb 25 17:50 gly_dynamics.in
-rw-r--r--  1 viktor viktor  743 Feb 25 17:50 gly_electrostatic.in
-rw-r--r--  1 viktor viktor  785 Feb 25 17:50 gly_energyforce.in
-rw-r--r--  1 viktor viktor 2.2K Feb 25 17:50 gly.pqr
-rw-r--r--  1 viktor viktor  51K Feb 25 17:50 gly.vert
drwxr-xr-x  2 viktor viktor   80 Feb 25 19:59 msms
-rw-r--r--  1 viktor viktor  821 Feb 25 17:50 README.md
-rw-r--r--  1 viktor viktor   14 Feb 25 17:50 traj_1_1.xyz
-rw-r--r--  1 viktor viktor   16 Feb 25 17:50 traj_1_2.xyz
-rw-r--r--  1 viktor viktor   19 Feb 25 17:50 traj_2_1.xyz
-rw-r--r--  1 viktor viktor   16 Feb 25 17:50 traj_2_2.xyz

./usr/share/apbs/examples/pbsam-gly/msms:
total 8.0K
drwxr-xr-x 2 viktor viktor   80 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  300 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  732 Feb 25 17:50 gly_electrostatic.in
-rw-r--r-- 1 viktor viktor 2.2K Feb 25 17:50 gly_msms.pqr

./usr/share/apbs/examples/pka-lig:
total 484K
drwxr-xr-x  3 viktor viktor  220 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 2.8K Feb 25 17:50 apbs-mol-surf.in
-rw-r--r--  1 viktor viktor 2.8K Feb 25 17:50 apbs-mol-vdw.in
-rw-r--r--  1 viktor viktor 2.8K Feb 25 17:50 apbs-smol-surf.in
-rw-r--r--  1 viktor viktor 2.8K Feb 25 17:50 apbs-smol-vdw.in
-rw-r--r--  1 viktor viktor 228K Feb 25 17:50 bx6_7_apo_apbs.pqr
-rw-r--r--  1 viktor viktor 231K Feb 25 17:50 bx6_7_bin_apbs.pqr
-rw-r--r--  1 viktor viktor 3.2K Feb 25 17:50 bx6_7_lig_apbs.pqr
-rw-r--r--  1 viktor viktor 3.9K Feb 25 17:50 README.md
drwxr-xr-x  2 viktor viktor  180 Feb 25 19:59 UHBD

./usr/share/apbs/examples/pka-lig/UHBD:
total 1012K
drwxr-xr-x 2 viktor viktor  180 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  220 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  906 Feb 25 17:50 README
-rw-r--r-- 1 viktor viktor 241K Feb 25 17:50 uhbd1-apo.out
-rw-r--r-- 1 viktor viktor 244K Feb 25 17:50 uhbd1-bin.out
-rw-r--r-- 1 viktor viktor  14K Feb 25 17:50 uhbd1-lig.out
-rw-r--r-- 1 viktor viktor 241K Feb 25 17:50 uhbd2-apo.out
-rw-r--r-- 1 viktor viktor 244K Feb 25 17:50 uhbd2-bin.out
-rw-r--r-- 1 viktor viktor  13K Feb 25 17:50 uhbd2-lig.out

./usr/share/apbs/examples/point-pmf:
total 72K
drwxr-xr-x  2 viktor viktor  400 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 1.4K Feb 25 17:50 apbs.in
-rw-r--r--  1 viktor viktor 1.4K Feb 25 17:50 complex-0_1.in
-rw-r--r--  1 viktor viktor  134 Feb 25 17:50 complex-0_1.pqr
-rw-r--r--  1 viktor viktor 1.4K Feb 25 17:50 complex-0_2.in
-rw-r--r--  1 viktor viktor  134 Feb 25 17:50 complex-0_2.pqr
-rw-r--r--  1 viktor viktor 1.4K Feb 25 17:50 complex-0_3.in
-rw-r--r--  1 viktor viktor  134 Feb 25 17:50 complex-0_3.pqr
-rw-r--r--  1 viktor viktor 1.4K Feb 25 17:50 complex-0_4.in
-rw-r--r--  1 viktor viktor  134 Feb 25 17:50 complex-0_4.pqr
-rw-r--r--  1 viktor viktor  998 Feb 25 17:50 energy.dat
-rw-r--r--  1 viktor viktor   67 Feb 25 17:50 mol0.pqr
-rw-r--r--  1 viktor viktor   67 Feb 25 17:50 mol1.pqr
-rw-r--r--  1 viktor viktor   67 Feb 25 17:50 mol2.pqr
-rw-r--r--  1 viktor viktor   67 Feb 25 17:50 mol3.pqr
-rw-r--r--  1 viktor viktor   67 Feb 25 17:50 mol4.pqr
-rw-r--r--  1 viktor viktor 1.4K Feb 25 17:50 point-pmf-0.in
-rw-r--r--  1 viktor viktor 1.4K Feb 25 17:50 README.md
-rw-r--r--  1 viktor viktor  593 Feb 25 17:50 runme.sh

./usr/share/apbs/examples/protein-rna:
total 196K
drwxr-xr-x  3 viktor viktor  340 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  770 Feb 25 17:50 apbs_unix_dx.py
-rw-r--r--  1 viktor viktor  870 Feb 25 17:50 apbs_win_dx.py
-rw-r--r--  1 viktor viktor   91 Feb 25 17:50 dxmath.txt
-rw-r--r--  1 viktor viktor 2.1K Feb 25 17:50 fit.py
-rw-r--r--  1 viktor viktor 1.6K Feb 25 17:50 Makefile.am
-rw-r--r--  1 viktor viktor  11K Feb 25 17:50 Makefile.in
-rw-r--r--  1 viktor viktor  43K Feb 25 17:50 model_outBoxB19.pqr
-rw-r--r--  1 viktor viktor  69K Feb 25 17:50 model_outNB.pqr
-rw-r--r--  1 viktor viktor  27K Feb 25 17:50 model_outNpep.pqr
drwxr-xr-x  2 viktor viktor  100 Feb 25 19:59 PDB
-rw-r--r--  1 viktor viktor  986 Feb 25 17:50 postprocess.sh
-rw-r--r--  1 viktor viktor 3.5K Feb 25 17:50 README.md
-rw-r--r--  1 viktor viktor  234 Feb 25 17:50 run_apdx_files.sh
-rw-r--r--  1 viktor viktor 1.6K Feb 25 17:50 template.txt
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 test.sh

./usr/share/apbs/examples/protein-rna/PDB:
total 164K
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor 340 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 50K Feb 25 17:50 model_outBoxB19.pdb
-rw-r--r-- 1 viktor viktor 80K Feb 25 17:50 model_outNB.pdb
-rw-r--r-- 1 viktor viktor 31K Feb 25 17:50 model_outNpep.pdb

./usr/share/apbs/examples/smpbe:
total 120K
drwxr-xr-x  2 viktor viktor  140 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 104K Feb 25 17:50 24dup.pqr
-rw-r--r--  1 viktor viktor  635 Feb 25 17:50 apbs-smpbe-24dup.in
-rw-r--r--  1 viktor viktor  566 Feb 25 17:50 apbs-smpbe-ion.in
-rw-r--r--  1 viktor viktor   66 Feb 25 17:50 ion.pqr
-rw-r--r--  1 viktor viktor  548 Feb 25 17:50 readme.md

./usr/share/apbs/examples/solv:
total 36K
drwxr-xr-x  3 viktor viktor  200 Feb 25 19:59 .
drwxr-xr-x 26 viktor viktor  540 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 2.4K Feb 25 17:50 apbs-mol.in
-rw-r--r--  1 viktor viktor 2.4K Feb 25 17:50 apbs-smol.in
-rw-r--r--  1 viktor viktor  674 Feb 25 17:50 Makefile.am
-rw-r--r--  1 viktor viktor  11K Feb 25 17:50 Makefile.in
-rw-r--r--  1 viktor viktor  216 Feb 25 17:50 methanol.pqr
-rw-r--r--  1 viktor viktor  144 Feb 25 17:50 methoxide.pqr
-rw-r--r--  1 viktor viktor 3.7K Feb 25 17:50 README.md
drwxr-xr-x  2 viktor viktor  100 Feb 25 19:59 UHBD

./usr/share/apbs/examples/solv/UHBD:
total 36K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  200 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  808 Feb 25 17:50 solv.dat.exam
-rw-r--r-- 1 viktor viktor 4.2K Feb 25 17:50 solv.inp.exam
-rw-r--r-- 1 viktor viktor  21K Feb 25 17:50 solv.out.orig.exam

./usr/share/apbs/tests:
total 32K
drwxr-xr-x 2 viktor viktor  140 Feb 25 19:59 .
drwxr-xr-x 6 viktor viktor  120 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 6.8K Feb 25 17:50 apbs_check_forces.py
-rw-r--r-- 1 viktor viktor 2.6K Feb 25 17:50 apbs_check_intermediate_energies.py
-rw-r--r-- 1 viktor viktor 2.1K Feb 25 17:50 apbs_check_results.py
-rw-r--r-- 1 viktor viktor  805 Feb 25 17:50 apbs_logger.py
-rw-r--r-- 1 viktor viktor  11K Feb 25 17:50 apbs_tester.py

./usr/share/apbs/tools:
total 4.0K
drwxr-xr-x 12 viktor viktor 260 Feb 25 19:59 .
drwxr-xr-x  6 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x  2 viktor viktor 380 Feb 25 19:59 bin
drwxr-xr-x  3 viktor viktor 120 Feb 25 19:59 conversion
drwxr-xr-x  2 viktor viktor  80 Feb 25 19:59 github
drwxr-xr-x  2 viktor viktor 120 Feb 25 19:59 manip
drwxr-xr-x  4 viktor viktor  80 Feb 25 19:59 matlab
drwxr-xr-x  2 viktor viktor 340 Feb 25 19:59 mesh
drwxr-xr-x  3 viktor viktor 120 Feb 25 19:59 osx
drwxr-xr-x  3 viktor viktor 280 Feb 25 19:59 python
-rw-r--r--  1 viktor viktor 120 Feb 25 17:50 README.html
drwxr-xr-x  3 viktor viktor  60 Feb 25 19:59 visualization
drwxr-xr-x  6 viktor viktor 140 Feb 25 19:59 windows

./usr/share/apbs/tools/bin:
total 612K
drwxr-xr-x  2 viktor viktor 380 Feb 25 19:59 .
drwxr-xr-x 12 viktor viktor 260 Feb 25 19:59 ..
-rwxr-xr-x  1 viktor viktor 42K Feb 25 19:58 analysis
-rwxr-xr-x  1 viktor viktor 27K Feb 25 19:58 benchmark
-rwxr-xr-x  1 viktor viktor 33K Feb 25 19:58 born
-rwxr-xr-x  1 viktor viktor 30K Feb 25 19:58 coulomb
-rwxr-xr-x  1 viktor viktor 27K Feb 25 19:58 del2dx
-rwxr-xr-x  1 viktor viktor 27K Feb 25 19:58 dx2mol
-rwxr-xr-x  1 viktor viktor 27K Feb 25 19:58 dx2uhbd
-rwxr-xr-x  1 viktor viktor 32K Feb 25 19:58 dxmath
-rwxr-xr-x  1 viktor viktor 53K Feb 25 19:58 mergedx
-rwxr-xr-x  1 viktor viktor 64K Feb 25 19:58 mergedx2
-rwxr-xr-x  1 viktor viktor 22K Feb 25 19:58 mgmesh
-rwxr-xr-x  1 viktor viktor 27K Feb 25 19:58 multivalue
-rwxr-xr-x  1 viktor viktor 63K Feb 25 19:58 similarity
-rwxr-xr-x  1 viktor viktor 33K Feb 25 19:58 smooth
-rwxr-xr-x  1 viktor viktor 27K Feb 25 19:58 tensor2dx
-rwxr-xr-x  1 viktor viktor 26K Feb 25 19:58 uhbd_asc2bin
-rwxr-xr-x  1 viktor viktor 25K Feb 25 19:58 value

./usr/share/apbs/tools/conversion:
total 16K
drwxr-xr-x  3 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 12 viktor viktor  260 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 1.4K Feb 25 17:50 amber2charmm.sh
drwxr-xr-x  4 viktor viktor   80 Feb 25 19:59 param
-rw-r--r--  1 viktor viktor  793 Feb 25 17:50 qcd2pqr.awk
-rw-r--r--  1 viktor viktor 7.0K Feb 25 17:50 WHATIF2AMBER.sed

./usr/share/apbs/tools/conversion/param:
total 0
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 pdb2pqr
drwxr-xr-x 2 viktor viktor  80 Feb 25 19:59 vparam

./usr/share/apbs/tools/conversion/param/pdb2pqr:
total 64K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 2.8K Feb 25 17:50 amber2uhbd.sh
-rw-r--r-- 1 viktor viktor  29K Feb 25 17:50 amber-param.dat
-rw-r--r-- 1 viktor viktor  897 Feb 25 17:50 c-alpha.dat
-rw-r--r-- 1 viktor viktor  21K Feb 25 17:50 weiner86-param.dat

./usr/share/apbs/tools/conversion/param/vparam:
total 416K
drwxr-xr-x 2 viktor viktor   80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  98K Feb 25 17:50 vparam-amber-parm94.dat
-rw-r--r-- 1 viktor viktor 314K Feb 25 17:50 vparam-amber-parm94.xml

./usr/share/apbs/tools/github:
total 12K
drwxr-xr-x  2 viktor viktor   80 Feb 25 19:59 .
drwxr-xr-x 12 viktor viktor  260 Feb 25 19:59 ..
-rwxr-xr-x  1 viktor viktor  868 Feb 25 17:50 getReleases.sh
-rw-r--r--  1 viktor viktor 5.0K Feb 25 17:50 release-data.py

./usr/share/apbs/tools/manip:
total 48K
drwxr-xr-x  2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 12 viktor viktor  260 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 7.5K Feb 25 17:50 born.c
-rw-r--r--  1 viktor viktor 6.1K Feb 25 17:50 coulomb.c
-rw-r--r--  1 viktor viktor  16K Feb 25 17:50 inputgen.py
-rw-r--r--  1 viktor viktor  14K Feb 25 17:50 psize.py

./usr/share/apbs/tools/matlab:
total 0
drwxr-xr-x  4 viktor viktor  80 Feb 25 19:59 .
drwxr-xr-x 12 viktor viktor 260 Feb 25 19:59 ..
drwxr-xr-x  2 viktor viktor  80 Feb 25 19:59 MAPBS
drwxr-xr-x 11 viktor viktor 360 Feb 25 19:59 solver

./usr/share/apbs/tools/matlab/MAPBS:
total 8.0K
drwxr-xr-x 2 viktor viktor   80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 1.9K Feb 25 17:50 License.txt
-rw-r--r-- 1 viktor viktor 3.2K Feb 25 17:50 README.txt

./usr/share/apbs/tools/matlab/solver:
total 432K
drwxr-xr-x 11 viktor viktor  360 Feb 25 19:59 .
drwxr-xr-x  4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 108K Feb 25 17:50 born-ion-model-example.pdf
-rw-r--r--  1 viktor viktor 8.5K Feb 25 17:50 born-ion-model-example.tex
drwxr-xr-x  8 viktor viktor  160 Feb 25 19:59 Examples
drwxr-xr-x  2 viktor viktor  160 Feb 25 19:59 MATLAB_PB_SOLVER_0
drwxr-xr-x  2 viktor viktor  200 Feb 25 19:59 MATLAB_PB_SOLVER_1
drwxr-xr-x  2 viktor viktor  200 Feb 25 19:59 MATLAB_PB_SOLVER_2
drwxr-xr-x  2 viktor viktor  220 Feb 25 19:59 MATLAB_PB_SOLVER_3
drwxr-xr-x  2 viktor viktor  240 Feb 25 19:59 MATLAB_PB_SOLVER_4
drwxr-xr-x  2 viktor viktor  360 Feb 25 19:59 MATLAB_PB_SOLVER_5
drwxr-xr-x  2 viktor viktor  580 Feb 25 19:59 MATLAB_PB_SOLVER_6
drwxr-xr-x  2 viktor viktor  440 Feb 25 19:59 MATLAB_PB_SOLVER_7
-rw-r--r--  1 viktor viktor 162K Feb 25 17:50 MATLAB_PB_SOLVER.pdf
-rw-r--r--  1 viktor viktor  13K Feb 25 17:50 MATLAB_PB_SOLVER.tex
-rw-r--r--  1 viktor viktor  134 Feb 25 17:50 README
-rw-r--r--  1 viktor viktor 114K Feb 25 17:50 two-ions-model-example.pdf
-rw-r--r--  1 viktor viktor 9.4K Feb 25 17:50 two-ions-model-example.tex

./usr/share/apbs/tools/matlab/solver/Examples:
total 0
drwxr-xr-x  8 viktor viktor 160 Feb 25 19:59 .
drwxr-xr-x 11 viktor viktor 360 Feb 25 19:59 ..
drwxr-xr-x  2 viktor viktor 120 Feb 25 19:59 born-ion
drwxr-xr-x  2 viktor viktor 140 Feb 25 19:59 DNA
drwxr-xr-x  2 viktor viktor 180 Feb 25 19:59 Meth
drwxr-xr-x  5 viktor viktor 180 Feb 25 19:59 pka
drwxr-xr-x  4 viktor viktor 100 Feb 25 19:59 point-pmf
drwxr-xr-x  2 viktor viktor 140 Feb 25 19:59 Two_ions_complex

./usr/share/apbs/tools/matlab/solver/Examples/born-ion:
total 16K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  160 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 1.8K Feb 25 17:50 born.in
-rw-r--r-- 1 viktor viktor   67 Feb 25 17:50 born-ion.pqr
-rw-r--r-- 1 viktor viktor  145 Feb 25 17:50 ref-born.inm
-rw-r--r-- 1 viktor viktor  172 Feb 25 17:50 solvated-born.inm

./usr/share/apbs/tools/matlab/solver/Examples/DNA:
total 236K
drwxr-xr-x 2 viktor viktor  140 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  160 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 111K Feb 25 17:50 DNA25.pdb.pqr
-rw-r--r-- 1 viktor viktor 1.5K Feb 25 17:50 DNA.in
-rw-r--r-- 1 viktor viktor 111K Feb 25 17:50 DNA_used_by_MATLAB.pqr
-rw-r--r-- 1 viktor viktor  136 Feb 25 17:50 ref-DNA.inm
-rw-r--r-- 1 viktor viktor  163 Feb 25 17:50 solvated-DNA.inm

./usr/share/apbs/tools/matlab/solver/Examples/Meth:
total 28K
drwxr-xr-x 2 viktor viktor  180 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  160 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  216 Feb 25 17:50 methanol.pqr
-rw-r--r-- 1 viktor viktor 3.5K Feb 25 17:50 meth.in
-rw-r--r-- 1 viktor viktor  144 Feb 25 17:50 methoxide.pqr
-rw-r--r-- 1 viktor viktor  161 Feb 25 17:50 ref-methanol.inm
-rw-r--r-- 1 viktor viktor  167 Feb 25 17:50 ref-methoxine.inm
-rw-r--r-- 1 viktor viktor  188 Feb 25 17:50 solvated-methanol.inm
-rw-r--r-- 1 viktor viktor  193 Feb 25 17:50 solvated-methoxine.inm

./usr/share/apbs/tools/matlab/solver/Examples/pka:
total 472K
drwxr-xr-x 5 viktor viktor  180 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  160 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 4.3K Feb 25 17:50 apbs-smol-vdw.in
-rw-r--r-- 1 viktor viktor 228K Feb 25 17:50 bx6_7_apo_apbs.pqr
-rw-r--r-- 1 viktor viktor 231K Feb 25 17:50 bx6_7_bin_apbs.pqr
-rw-r--r-- 1 viktor viktor 3.2K Feb 25 17:50 bx6_7_lig_apbs.pqr
drwxr-xr-x 4 viktor viktor  120 Feb 25 19:59 complex
drwxr-xr-x 4 viktor viktor  120 Feb 25 19:59 kinase
drwxr-xr-x 4 viktor viktor  120 Feb 25 19:59 ligand

./usr/share/apbs/tools/matlab/solver/Examples/pka/complex:
total 8.0K
drwxr-xr-x 4 viktor viktor 120 Feb 25 19:59 .
drwxr-xr-x 5 viktor viktor 180 Feb 25 19:59 ..
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 coarse-complex_model
-rw-r--r-- 1 viktor viktor 300 Feb 25 17:50 complex.inm
-rw-r--r-- 1 viktor viktor 318 Feb 25 17:50 focusname.inm
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 target-complex_model

./usr/share/apbs/tools/matlab/solver/Examples/pka/complex/coarse-complex_model:
total 0
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_coarse_grid
drwxr-xr-x 2 viktor viktor  80 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/pka/complex/coarse-complex_model/COMPARATIVE_ANALYSIS_coarse_grid:
total 812K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 211K Feb 25 17:50 absolute_error_coarse_grid_complex.jpg
-rw-r--r-- 1 viktor viktor 139K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 284K Feb 25 17:50 coarse-complex-pot.dx_and_coarse_grid_MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 176K Feb 25 17:50 coarse-complex-pot.dx_and_coarse_grid_MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/complex/coarse-complex_model/outputfiles:
total 324K
drwxr-xr-x 2 viktor viktor   80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 145K Feb 25 17:50 coarse_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor 175K Feb 25 17:50 coarse_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/complex/target-complex_model:
total 0
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_target_grid
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/pka/complex/target-complex_model/COMPARATIVE_ANALYSIS_target_grid:
total 748K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 139K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 157K Feb 25 17:50 absolute_error_target_grid_complex.jpg
-rw-r--r-- 1 viktor viktor 278K Feb 25 17:50 complex-pot.dx_and_target_grid__MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 166K Feb 25 17:50 complex-pot.dx_and_target_grid__MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/complex/target-complex_model/outputfiles:
total 316K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 2.3K Feb 25 17:50 MATLAB_screen.io
-rw-r--r-- 1 viktor viktor 144K Feb 25 17:50 target_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor 167K Feb 25 17:50 target_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/kinase:
total 8.0K
drwxr-xr-x 4 viktor viktor 120 Feb 25 19:59 .
drwxr-xr-x 5 viktor viktor 180 Feb 25 19:59 ..
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 coarse_kpa_model
-rw-r--r-- 1 viktor viktor 298 Feb 25 17:50 focusname.inm
-rw-r--r-- 1 viktor viktor 280 Feb 25 17:50 pka.inm
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 target_kpa_model

./usr/share/apbs/tools/matlab/solver/Examples/pka/kinase/coarse_kpa_model:
total 0
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_coarse_grid
drwxr-xr-x 2 viktor viktor  80 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/pka/kinase/coarse_kpa_model/COMPARATIVE_ANALYSIS_coarse_grid:
total 812K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 211K Feb 25 17:50 absolute_error_coarse_grid_pka.jpg
-rw-r--r-- 1 viktor viktor 139K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 284K Feb 25 17:50 coarse-pka-pot.dx_and_coarse_grid_MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 176K Feb 25 17:50 coarse-pka-pot.dx_and_coarse_grid_MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/kinase/coarse_kpa_model/outputfiles:
total 324K
drwxr-xr-x 2 viktor viktor   80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 145K Feb 25 17:50 coarse_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor 175K Feb 25 17:50 coarse_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/kinase/target_kpa_model:
total 0
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_target_grid
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/pka/kinase/target_kpa_model/COMPARATIVE_ANALYSIS_target_grid:
total 744K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 139K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 156K Feb 25 17:50 absolute_error_target_pka.jpg
-rw-r--r-- 1 viktor viktor 278K Feb 25 17:50 pka-pot.dx_and_target_grid__MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 166K Feb 25 17:50 pka-pot.dx_and_target_grid__MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/kinase/target_kpa_model/outputfiles:
total 316K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 2.3K Feb 25 17:50 MATLAB_screen.io
-rw-r--r-- 1 viktor viktor 144K Feb 25 17:50 target_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor 168K Feb 25 17:50 target_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/ligand:
total 8.0K
drwxr-xr-x 4 viktor viktor 120 Feb 25 19:59 .
drwxr-xr-x 5 viktor viktor 180 Feb 25 19:59 ..
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 coarse_ligand_model
-rw-r--r-- 1 viktor viktor 313 Feb 25 17:50 focusname.inm
-rw-r--r-- 1 viktor viktor 295 Feb 25 17:50 ligand.inm
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 target_ligand_model

./usr/share/apbs/tools/matlab/solver/Examples/pka/ligand/coarse_ligand_model:
total 0
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_coarse_grid
drwxr-xr-x 2 viktor viktor  80 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/pka/ligand/coarse_ligand_model/COMPARATIVE_ANALYSIS_coarse_grid:
total 744K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 154K Feb 25 17:50 absolute_error_coarse_grid_ligand.jpg
-rw-r--r-- 1 viktor viktor 140K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 283K Feb 25 17:50 coarse-ligand-pot.dx_and_coarse_grid_MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 164K Feb 25 17:50 coarse-ligand-pot.dx_and_coarse_grid_MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/ligand/coarse_ligand_model/outputfiles:
total 316K
drwxr-xr-x 2 viktor viktor   80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 142K Feb 25 17:50 coarse_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor 172K Feb 25 17:50 coarse_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/ligand/target_ligand_model:
total 0
drwxr-xr-x 4 viktor viktor  80 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 120 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_target_grid
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/pka/ligand/target_ligand_model/COMPARATIVE_ANALYSIS_target_grid:
total 692K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 140K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 136K Feb 25 17:50 absolute_error_target_ligand.jpg
-rw-r--r-- 1 viktor viktor 283K Feb 25 17:50 ligand-pot.dx_and_target_grid__MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 132K Feb 25 17:50 ligand-pot.dx_and_target_grid__MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/pka/ligand/target_ligand_model/outputfiles:
total 276K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor   80 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 2.4K Feb 25 17:50 MATLAB_screen.io
-rw-r--r-- 1 viktor viktor 142K Feb 25 17:50 target_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor 125K Feb 25 17:50 target_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf:
total 4.0K
drwxr-xr-x 4 viktor viktor 100 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor 160 Feb 25 19:59 ..
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 -0.25
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 -2.75
-rw-r--r-- 1 viktor viktor 526 Feb 25 17:50 ENERGY_TABLE.txt

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25:
total 28K
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 100 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_mole1
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_mole1mole2
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_mole2
-rw-r--r-- 1 viktor viktor 275 Feb 25 17:50 mole1.inm
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 mole1_model
-rw-r--r-- 1 viktor viktor 305 Feb 25 17:50 mole1mole2.inm
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 mole1mole2_model
-rw-r--r-- 1 viktor viktor 136 Feb 25 17:50 mole1mole2.pqr
-rw-r--r-- 1 viktor viktor  68 Feb 25 17:50 mole1.pqr
-rw-r--r-- 1 viktor viktor 275 Feb 25 17:50 mole2.inm
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 mole2_model
-rw-r--r-- 1 viktor viktor  68 Feb 25 17:50 mole2.pqr
-rw-r--r-- 1 viktor viktor  67 Feb 25 17:50 molex.pqr

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25/COMPARATIVE_ANALYSIS_mole1:
total 408K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  300 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  49K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 103K Feb 25 17:50 absolute_error.jpg
-rw-r--r-- 1 viktor viktor 116K Feb 25 17:50 mole1-pot.dx_and_target_grid__MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 135K Feb 25 17:50 mole1-pot.dx_and_target_grid__MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25/COMPARATIVE_ANALYSIS_mole1mole2:
total 412K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  300 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  46K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 122K Feb 25 17:50 absolute_error.jpg
-rw-r--r-- 1 viktor viktor 114K Feb 25 17:50 mole1mole2-pot.dx_and_target_grid__MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 124K Feb 25 17:50 mole1mole2-pot.dx_and_target_grid__MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25/COMPARATIVE_ANALYSIS_mole2:
total 400K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  300 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  41K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 118K Feb 25 17:50 absolute_error.jpg
-rw-r--r-- 1 viktor viktor 115K Feb 25 17:50 mole2-pot.dx_and_target_grid__MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 119K Feb 25 17:50 mole2-pot.dx_and_target_grid__MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25/mole1_model:
total 0
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25/mole1_model/outputfiles:
total 168K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor   60 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 1.2K Feb 25 17:50 MATLAB_screen.io
-rw-r--r-- 1 viktor viktor  63K Feb 25 17:50 target_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor 100K Feb 25 17:50 target_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25/mole1mole2_model:
total 0
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25/mole1mole2_model/outputfiles:
total 160K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor   60 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 1.3K Feb 25 17:50 MATLAB_screen.io
-rw-r--r-- 1 viktor viktor  62K Feb 25 17:50 target_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor  89K Feb 25 17:50 target_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25/mole2_model:
total 0
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-0.25/mole2_model/outputfiles:
total 156K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor   60 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 1.2K Feb 25 17:50 MATLAB_screen.io
-rw-r--r-- 1 viktor viktor  63K Feb 25 17:50 target_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor  87K Feb 25 17:50 target_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75:
total 28K
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 .
drwxr-xr-x 4 viktor viktor 100 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_mole1
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_mole1mole2
drwxr-xr-x 2 viktor viktor 120 Feb 25 19:59 COMPARATIVE_ANALYSIS_mole2
-rw-r--r-- 1 viktor viktor 275 Feb 25 17:50 mole1.inm
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 mole1_model
-rw-r--r-- 1 viktor viktor 305 Feb 25 17:50 mole1mole2.inm
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 mole1mole2_model
-rw-r--r-- 1 viktor viktor 136 Feb 25 17:50 mole1mole2.pqr
-rw-r--r-- 1 viktor viktor  68 Feb 25 17:50 mole1.pqr
-rw-r--r-- 1 viktor viktor 275 Feb 25 17:50 mole2.inm
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 mole2_model
-rw-r--r-- 1 viktor viktor  68 Feb 25 17:50 mole2.pqr
-rw-r--r-- 1 viktor viktor  67 Feb 25 17:50 molex.pqr

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75/COMPARATIVE_ANALYSIS_mole1:
total 408K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  300 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  49K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 103K Feb 25 17:50 absolute_error.jpg
-rw-r--r-- 1 viktor viktor 116K Feb 25 17:50 mole1-pot.dx_and_target_grid__MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 135K Feb 25 17:50 mole1-pot.dx_and_target_grid__MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75/COMPARATIVE_ANALYSIS_mole1mole2:
total 392K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  300 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  47K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor  98K Feb 25 17:50 absolute_error.jpg
-rw-r--r-- 1 viktor viktor 114K Feb 25 17:50 mole1mole2-pot.dx_and_target_grid__MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 128K Feb 25 17:50 mole1mole2-pot.dx_and_target_grid__MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75/COMPARATIVE_ANALYSIS_mole2:
total 392K
drwxr-xr-x 2 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  300 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  47K Feb 25 17:50 absolute_error.fig
-rw-r--r-- 1 viktor viktor 103K Feb 25 17:50 absolute_error.jpg
-rw-r--r-- 1 viktor viktor 115K Feb 25 17:50 mole2-pot.dx_and_target_grid__MATLAB_pot.dx.fig
-rw-r--r-- 1 viktor viktor 123K Feb 25 17:50 mole2-pot.dx_and_target_grid__MATLAB_pot.dx.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75/mole1_model:
total 0
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75/mole1_model/outputfiles:
total 168K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor   60 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 1.2K Feb 25 17:50 MATLAB_screen.io
-rw-r--r-- 1 viktor viktor  63K Feb 25 17:50 target_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor 100K Feb 25 17:50 target_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75/mole1mole2_model:
total 0
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75/mole1mole2_model/outputfiles:
total 164K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor   60 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 1.3K Feb 25 17:50 MATLAB_screen.io
-rw-r--r-- 1 viktor viktor  63K Feb 25 17:50 target_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor  94K Feb 25 17:50 target_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75/mole2_model:
total 0
drwxr-xr-x 3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor 300 Feb 25 19:59 ..
drwxr-xr-x 2 viktor viktor 100 Feb 25 19:59 outputfiles

./usr/share/apbs/tools/matlab/solver/Examples/point-pmf/-2.75/mole2_model/outputfiles:
total 160K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor   60 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 1.2K Feb 25 17:50 MATLAB_screen.io
-rw-r--r-- 1 viktor viktor  61K Feb 25 17:50 target_grid_MATLAB_pot.fig
-rw-r--r-- 1 viktor viktor  90K Feb 25 17:50 target_grid_MATLAB_pot.jpg

./usr/share/apbs/tools/matlab/solver/Examples/Two_ions_complex:
total 8.0M
drwxr-xr-x 2 viktor viktor  140 Feb 25 19:59 .
drwxr-xr-x 8 viktor viktor  160 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  160 Feb 25 17:50 ref-two-ions.inm
-rw-r--r-- 1 viktor viktor  187 Feb 25 17:50 solvated-two-ions.inm
-rw-r--r-- 1 viktor viktor 2.4K Feb 25 17:50 TwoIons.in
-rw-r--r-- 1 viktor viktor  138 Feb 25 17:50 twoions.pqr
-rw-r--r-- 1 viktor viktor 8.0M Feb 25 17:50 Two_Ions.zip

./usr/share/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_0:
total 28K
drwxr-xr-x  2 viktor viktor  160 Feb 25 19:59 .
drwxr-xr-x 11 viktor viktor  360 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 2.0K Feb 25 17:50 BoundaryCondition.m
-rw-r--r--  1 viktor viktor 3.4K Feb 25 17:50 BuildA.m
-rw-r--r--  1 viktor viktor  720 Feb 25 17:50 data_parse.m
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 dx_export.m
-rw-r--r--  1 viktor viktor 6.0K Feb 25 17:50 main.m
-rw-r--r--  1 viktor viktor  949 Feb 25 17:50 read_inm.m

./usr/share/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_1:
total 36K
drwxr-xr-x  2 viktor viktor  200 Feb 25 19:59 .
drwxr-xr-x 11 viktor viktor  360 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 2.0K Feb 25 17:50 BoundaryCondition.m
-rw-r--r--  1 viktor viktor 3.4K Feb 25 17:50 BuildA.m
-rw-r--r--  1 viktor viktor 3.6K Feb 25 17:50 comparison.m
-rw-r--r--  1 viktor viktor  710 Feb 25 17:50 data_parse.m
-rw-r--r--  1 viktor viktor 1.9K Feb 25 17:50 discretization.m
-rw-r--r--  1 viktor viktor 1.7K Feb 25 17:50 dx_export.m
-rw-r--r--  1 viktor viktor 5.8K Feb 25 17:50 main.m
-rw-r--r--  1 viktor viktor  846 Feb 25 17:50 read_inm.m

./usr/share/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_2:
total 36K
drwxr-xr-x  2 viktor viktor  200 Feb 25 19:59 .
drwxr-xr-x 11 viktor viktor  360 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 2.0K Feb 25 17:50 BoundaryCondition.m
-rw-r--r--  1 viktor viktor 3.5K Feb 25 17:50 BuildA.m
-rw-r--r--  1 viktor viktor 3.5K Feb 25 17:50 comparison.m
-rw-r--r--  1 viktor viktor  710 Feb 25 17:50 data_parse.m
-rw-r--r--  1 viktor viktor 1.9K Feb 25 17:50 discretization.m
-rw-r--r--  1 viktor viktor 1.7K Feb 25 17:50 dx_export.m
-rw-r--r--  1 viktor viktor 5.8K Feb 25 17:50 main.m
-rw-r--r--  1 viktor viktor  963 Feb 25 17:50 read_inm.m

./usr/share/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_3:
total 44K
drwxr-xr-x  2 viktor viktor  220 Feb 25 19:59 .
drwxr-xr-x 11 viktor viktor  360 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 2.0K Feb 25 17:50 BoundaryCondition.m
-rw-r--r--  1 viktor viktor 3.5K Feb 25 17:50 BuildA.m
-rw-r--r--  1 viktor viktor 3.5K Feb 25 17:50 comparison.m
-rw-r--r--  1 viktor viktor 4.1K Feb 25 17:50 comparison_reaction_field.m
-rw-r--r--  1 viktor viktor  710 Feb 25 17:50 data_parse.m
-rw-r--r--  1 viktor viktor 2.4K Feb 25 17:50 discretization.m
-rw-r--r--  1 viktor viktor 1.7K Feb 25 17:50 dx_export.m
-rw-r--r--  1 viktor viktor 6.0K Feb 25 17:50 main.m
-rw-r--r--  1 viktor viktor  963 Feb 25 17:50 read_inm.m

./usr/share/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_4:
total 48K
drwxr-xr-x  2 viktor viktor  240 Feb 25 19:59 .
drwxr-xr-x 11 viktor viktor  360 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 2.0K Feb 25 17:50 BoundaryCondition.m
-rw-r--r--  1 viktor viktor 3.5K Feb 25 17:50 BuildA.m
-rw-r--r--  1 viktor viktor 3.5K Feb 25 17:50 comparison.m
-rw-r--r--  1 viktor viktor 4.2K Feb 25 17:50 comparison_reaction_field.m
-rw-r--r--  1 viktor viktor  710 Feb 25 17:50 data_parse.m
-rw-r--r--  1 viktor viktor 2.4K Feb 25 17:50 discretization.m
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 dx_export.m
-rw-r--r--  1 viktor viktor  555 Feb 25 17:50 gridinf.m
-rw-r--r--  1 viktor viktor 6.1K Feb 25 17:50 main.m
-rw-r--r--  1 viktor viktor  963 Feb 25 17:50 read_inm.m

./usr/share/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_5:
total 296K
drwxr-xr-x  2 viktor viktor  360 Feb 25 19:59 .
drwxr-xr-x 11 viktor viktor  360 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 1.5K Feb 25 17:50 BoundaryCondition.m
-rw-r--r--  1 viktor viktor 3.3K Feb 25 17:50 BuildA.m
-rw-r--r--  1 viktor viktor  926 Feb 25 17:50 centerofgrid.m
-rw-r--r--  1 viktor viktor 3.6K Feb 25 17:50 comparison.m
-rw-r--r--  1 viktor viktor 4.2K Feb 25 17:50 comparison_reaction_field.m
-rw-r--r--  1 viktor viktor  710 Feb 25 17:50 data_parse.m
-rw-r--r--  1 viktor viktor 2.2K Feb 25 17:50 discretization.m
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 dx_export.m
-rw-r--r--  1 viktor viktor  20K Feb 25 17:50 fbc.m
-rw-r--r--  1 viktor viktor  555 Feb 25 17:50 gridinf.m
-rw-r--r--  1 viktor viktor  13K Feb 25 17:50 MAPBS.m
-rw-r--r--  1 viktor viktor 183K Feb 25 17:50 MATLAB_PB_SOLVER_5.pdf
-rw-r--r--  1 viktor viktor  19K Feb 25 17:50 MATLAB_PB_SOLVER_5.tex
-rw-r--r--  1 viktor viktor  512 Feb 25 17:50 parameters.m
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 read_inm.m
-rw-r--r--  1 viktor viktor 4.1K Feb 25 17:50 Readme.txt

./usr/share/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_6:
total 1.8M
drwxr-xr-x  2 viktor viktor  580 Feb 25 19:59 .
drwxr-xr-x 11 viktor viktor  360 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 1.5K Feb 25 17:50 BoundaryCondition.m
-rw-r--r--  1 viktor viktor 3.3K Feb 25 17:50 BuildA.m
-rw-r--r--  1 viktor viktor  926 Feb 25 17:50 centerofgrid.m
-rw-r--r--  1 viktor viktor 3.6K Feb 25 17:50 comparison.m
-rw-r--r--  1 viktor viktor 7.1K Feb 25 17:50 comparison_pot.fig
-rw-r--r--  1 viktor viktor  12K Feb 25 17:50 comparison_pot.m
-rw-r--r--  1 viktor viktor 4.2K Feb 25 17:50 comparison_reaction_field.m
-rw-r--r--  1 viktor viktor  710 Feb 25 17:50 data_parse.m
-rw-r--r--  1 viktor viktor 2.2K Feb 25 17:50 discretization.m
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 dx_export.m
-rw-r--r--  1 viktor viktor 1.7K Feb 25 17:50 energy.m
-rw-r--r--  1 viktor viktor  20K Feb 25 17:50 fbc.m
-rw-r--r--  1 viktor viktor  555 Feb 25 17:50 gridinf.m
-rw-r--r--  1 viktor viktor  15K Feb 25 17:50 inmcreator.fig
-rw-r--r--  1 viktor viktor  26K Feb 25 17:50 inmcreator.m
-rw-r--r--  1 viktor viktor 5.8K Feb 25 17:50 mapbs_comparison.m
-rw-r--r--  1 viktor viktor  14K Feb 25 17:50 MAPBS.m
-rw-r--r--  1 viktor viktor  15K Feb 25 17:50 MATLAB_APBS.fig
-rw-r--r--  1 viktor viktor  15K Feb 25 17:50 MATLAB_APBS_FOCUS.fig
-rw-r--r--  1 viktor viktor  30K Feb 25 17:50 MATLAB_APBS_FOCUS.m
-rw-r--r--  1 viktor viktor  30K Feb 25 17:50 MATLAB_APBS.m
-rw-r--r--  1 viktor viktor 216K Feb 25 17:50 MATLAB_PB_SOLVER_6.pdf
-rw-r--r--  1 viktor viktor  27K Feb 25 17:50 MATLAB_PB_SOLVER_6.tex
-rw-r--r--  1 viktor viktor 1.3M Feb 25 17:50 MATLAB_PB_SOLVER_AND_GUI.pdf
-rw-r--r--  1 viktor viktor  512 Feb 25 17:50 parameters.m
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 read_inm.m
-rw-r--r--  1 viktor viktor 1.7K Feb 25 17:50 Readme.txt

./usr/share/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_7:
total 1.7M
drwxr-xr-x  2 viktor viktor  440 Feb 25 19:59 .
drwxr-xr-x 11 viktor viktor  360 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 1.6K Feb 25 17:50 BoundaryCondition.m
-rw-r--r--  1 viktor viktor 5.1K Feb 25 17:50 BuildA.m
-rw-r--r--  1 viktor viktor  926 Feb 25 17:50 centerofgrid.m
-rw-r--r--  1 viktor viktor 7.1K Feb 25 17:50 comparison_pot.fig
-rw-r--r--  1 viktor viktor  12K Feb 25 17:50 comparison_pot.m
-rw-r--r--  1 viktor viktor  710 Feb 25 17:50 data_parse.m
-rw-r--r--  1 viktor viktor 2.2K Feb 25 17:50 discretization.m
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 dx_export.m
-rw-r--r--  1 viktor viktor 1.7K Feb 25 17:50 energy.m
-rw-r--r--  1 viktor viktor  20K Feb 25 17:50 fbc.m
-rw-r--r--  1 viktor viktor  555 Feb 25 17:50 gridinf.m
-rw-r--r--  1 viktor viktor 5.8K Feb 25 17:50 mapbs_comparison.m
-rw-r--r--  1 viktor viktor  19K Feb 25 17:50 MAPBS.m
-rw-r--r--  1 viktor viktor  16K Feb 25 17:50 MATLAB_APBS.fig
-rw-r--r--  1 viktor viktor  16K Feb 25 17:50 MATLAB_APBS_FOCUS.fig
-rw-r--r--  1 viktor viktor  30K Feb 25 17:50 MATLAB_APBS_FOCUS.m
-rw-r--r--  1 viktor viktor  31K Feb 25 17:50 MATLAB_APBS.m
-rw-r--r--  1 viktor viktor 1.4M Feb 25 17:50 MATLAB_PB_SOLVER_AND_GUI.pdf
-rw-r--r--  1 viktor viktor  512 Feb 25 17:50 parameters.m
-rw-r--r--  1 viktor viktor 1.3K Feb 25 17:50 read_inm.m

./usr/share/apbs/tools/mesh:
total 168K
drwxr-xr-x  2 viktor viktor  340 Feb 25 19:59 .
drwxr-xr-x 12 viktor viktor  260 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor  11K Feb 25 17:50 analysis.c
-rw-r--r--  1 viktor viktor 3.5K Feb 25 17:50 benchmark.c
-rw-r--r--  1 viktor viktor 5.4K Feb 25 17:50 del2dx.c
-rw-r--r--  1 viktor viktor 5.1K Feb 25 17:50 dx2mol.c
-rw-r--r--  1 viktor viktor 4.5K Feb 25 17:50 dx2uhbd.c
-rw-r--r--  1 viktor viktor  13K Feb 25 17:50 dxmath.c
-rw-r--r--  1 viktor viktor  21K Feb 25 17:50 mergedx2.c
-rw-r--r--  1 viktor viktor  19K Feb 25 17:50 mergedx.c
-rw-r--r--  1 viktor viktor 1.7K Feb 25 17:50 mgmesh.c
-rw-r--r--  1 viktor viktor 8.2K Feb 25 17:50 multivalue.c
-rw-r--r--  1 viktor viktor  23K Feb 25 17:50 similarity.c
-rw-r--r--  1 viktor viktor 9.9K Feb 25 17:50 smooth.c
-rw-r--r--  1 viktor viktor 5.5K Feb 25 17:50 tensor2dx.c
-rw-r--r--  1 viktor viktor 3.4K Feb 25 17:50 uhbd_asc2bin.c
-rw-r--r--  1 viktor viktor 3.8K Feb 25 17:50 value.c

./usr/share/apbs/tools/osx:
total 12K
drwxr-xr-x  3 viktor viktor  120 Feb 25 19:59 .
drwxr-xr-x 12 viktor viktor  260 Feb 25 19:59 ..
drwxr-xr-x  2 viktor viktor  240 Feb 25 19:59 APBS.iconset
-rw-r--r--  1 viktor viktor  224 Feb 25 17:50 apbs_term
-rw-r--r--  1 viktor viktor 1.6K Feb 25 17:50 info.plist
-rw-r--r--  1 viktor viktor  733 Feb 25 17:50 patch_binary.sh

./usr/share/apbs/tools/osx/APBS.iconset:
total 440K
drwxr-xr-x 2 viktor viktor  240 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  120 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  37K Feb 25 17:50 icon_128x128@2x.png
-rw-r--r-- 1 viktor viktor  16K Feb 25 17:50 icon_128x128.png
-rw-r--r-- 1 viktor viktor 1.5K Feb 25 17:50 icon_16x16@2x.png
-rw-r--r-- 1 viktor viktor  710 Feb 25 17:50 icon_16x16.png
-rw-r--r-- 1 viktor viktor  78K Feb 25 17:50 icon_256x256@2x.png
-rw-r--r-- 1 viktor viktor  37K Feb 25 17:50 icon_256x256.png
-rw-r--r-- 1 viktor viktor 3.0K Feb 25 17:50 icon_32x32@2x.png
-rw-r--r-- 1 viktor viktor 1.5K Feb 25 17:50 icon_32x32.png
-rw-r--r-- 1 viktor viktor 167K Feb 25 17:50 icon_512x512@2x.png
-rw-r--r-- 1 viktor viktor  78K Feb 25 17:50 icon_512x512.png

./usr/share/apbs/tools/python:
total 384K
drwxr-xr-x  3 viktor viktor  280 Feb 25 19:59 .
drwxr-xr-x 12 viktor viktor  260 Feb 25 19:59 ..
-rw-r--r--  1 viktor viktor 6.0K Feb 25 17:50 apbs.in
-rw-r--r--  1 viktor viktor 255K Feb 25 17:50 apbslib.c
-rw-r--r--  1 viktor viktor  15K Feb 25 17:50 apbslib.i
-rw-r--r--  1 viktor viktor  12K Feb 25 17:50 apbslib_wrap.doc
-rw-r--r--  1 viktor viktor   66 Feb 25 17:50 ion.pqr
-rw-r--r--  1 viktor viktor  14K Feb 25 17:50 main.py
-rw-r--r--  1 viktor viktor  21K Feb 25 17:50 Makefile
-rw-r--r--  1 viktor viktor  898 Feb 25 17:50 Makefile.am
-rw-r--r--  1 viktor viktor  20K Feb 25 17:50 Makefile.in
-rw-r--r--  1 viktor viktor  18K Feb 25 17:50 noinput.py
-rw-r--r--  1 viktor viktor 1.8K Feb 25 17:50 README
drwxr-xr-x  2 viktor viktor  240 Feb 25 19:59 vgrid

./usr/share/apbs/tools/python/vgrid:
total 172K
drwxr-xr-x 2 viktor viktor  240 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor  280 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 3.0K Feb 25 17:50 average.py
-rw-r--r-- 1 viktor viktor  16K Feb 25 17:50 Makefile
-rw-r--r-- 1 viktor viktor  845 Feb 25 17:50 Makefile.am
-rw-r--r-- 1 viktor viktor  15K Feb 25 17:50 Makefile.in
-rw-r--r-- 1 viktor viktor  14K Feb 25 17:50 mergedx.py
-rw-r--r-- 1 viktor viktor 1.6K Feb 25 17:50 README
-rw-r--r-- 1 viktor viktor 2.3K Feb 25 17:50 read.py
-rw-r--r-- 1 viktor viktor 3.0K Feb 25 17:50 vgrid.i
-rw-r--r-- 1 viktor viktor  95K Feb 25 17:50 vgridlib.c
-rw-r--r-- 1 viktor viktor 4.4K Feb 25 17:50 vgrid.py

./usr/share/apbs/tools/visualization:
total 0
drwxr-xr-x  3 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 12 viktor viktor 260 Feb 25 19:59 ..
drwxr-xr-x  2 viktor viktor 240 Feb 25 19:59 opendx

./usr/share/apbs/tools/visualization/opendx:
total 156K
drwxr-xr-x 2 viktor viktor  240 Feb 25 19:59 .
drwxr-xr-x 3 viktor viktor   60 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 3.1K Feb 25 17:50 multipot.cfg
-rw-r--r-- 1 viktor viktor  34K Feb 25 17:50 multipot.net
-rw-r--r-- 1 viktor viktor 5.4K Feb 25 17:50 potacc.cfg
-rw-r--r-- 1 viktor viktor  538 Feb 25 17:50 potacc.cm
-rw-r--r-- 1 viktor viktor  31K Feb 25 17:50 potacc.net
-rw-r--r-- 1 viktor viktor 5.8K Feb 25 17:50 pot.cfg
-rw-r--r-- 1 viktor viktor  471 Feb 25 17:50 pot.cm
-rw-r--r-- 1 viktor viktor  30K Feb 25 17:50 pot.net
-rw-r--r-- 1 viktor viktor 2.5K Feb 25 17:50 surface.cfg
-rw-r--r-- 1 viktor viktor  21K Feb 25 17:50 surface.net

./usr/share/apbs/tools/windows:
total 4.0K
drwxr-xr-x  6 viktor viktor 140 Feb 25 19:59  .
drwxr-xr-x 12 viktor viktor 260 Feb 25 19:59  ..
drwxr-xr-x  2 viktor viktor  60 Feb 25 19:59 'command-line support'
drwxr-xr-x  2 viktor viktor  80 Feb 25 19:59 'configuration headers'
drwxr-xr-x  2 viktor viktor  60 Feb 25 19:59 'NSI configuration'
-rw-r--r--  1 viktor viktor 138 Feb 25 17:50  README.txt
drwxr-xr-x  2 viktor viktor 100 Feb 25 19:59 'visual studio property pages'

'./usr/share/apbs/tools/windows/command-line support':
total 4.0K
drwxr-xr-x 2 viktor viktor  60 Feb 25 19:59 .
drwxr-xr-x 6 viktor viktor 140 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor  32 Feb 25 17:50 apbs-cli.bat

'./usr/share/apbs/tools/windows/configuration headers':
total 16K
drwxr-xr-x 2 viktor viktor   80 Feb 25 19:59 .
drwxr-xr-x 6 viktor viktor  140 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 2.7K Feb 25 17:50 apbscfg.h
-rw-r--r-- 1 viktor viktor 9.3K Feb 25 17:50 maloccf.h

'./usr/share/apbs/tools/windows/NSI configuration':
total 8.0K
drwxr-xr-x 2 viktor viktor   60 Feb 25 19:59 .
drwxr-xr-x 6 viktor viktor  140 Feb 25 19:59 ..
-rw-r--r-- 1 viktor viktor 6.3K Feb 25 17:50 apbs.nsi

'./usr/share/apbs/tools/windows/visual studio property pages':
total 12K
drwxr-xr-x 2 viktor viktor  100 Feb 25 19:59  .
drwxr-xr-x 6 viktor viktor  140 Feb 25 19:59  ..
-rw-r--r-- 1 viktor viktor  408 Feb 25 17:50 'Debug build properties.props'
-rw-r--r-- 1 viktor viktor 2.3K Feb 25 17:50 'Generic build properties.props'
-rw-r--r-- 1 viktor viktor  403 Feb 25 17:50 'Release build properties.props'

I can't find, for example, all extra binaries in /tmp/dist/usr/bin, _apbslib.so and so on. Seems like install target doesn't install all stuff properly.

One more thing to note. During cmake stage it complains about rpc/rpc.h not being found. Seems like it searches only in /usr/include by default while modern Linux distributions now provide SunRPC replacement - TIRPC. It stores all headers in /usr/include/tirpc but cmake script can't find them. May be it worth to add FindTIRPC.cmake, for example into apbs/externals/fetk/maloc/cmake/modules with the following content:

# FindTIRPC
# ---------
#
# Find the native TIRPC includes and library.
#
# Result Variables
# ^^^^^^^^^^^^^^^^
#
# This module will set the following variables in your project:
#
# ``TIRPC_INCLUDE_DIRS``
#   where to find rpc.h, etc.
# ``TIRPC_LIBRARIES``
#   the libraries to link against to use TIRPC.
# ``TIRPC_VERSION``
#   the version of TIRPC found.
# ``TIRPC_FOUND``
#   true if the TIRPC headers and libraries were found.
#

find_package(PkgConfig QUIET)
pkg_check_modules(PC_TIRPC libtirpc)

find_path(TIRPC_INCLUDE_DIRS
    NAMES netconfig.h
    PATH_SUFFIXES tirpc
    HINTS ${PC_TIRPC_INCLUDE_DIRS}
)

find_library(TIRPC_LIBRARIES
    NAMES tirpc
    HINTS ${PC_TIRPC_LIBRARY_DIRS}
)

set(TIRPC_VERSION ${PC_TIRPC_VERSION})

include(FindPackageHandleStandardArgs)

find_package_handle_standard_args(TIRPC
    REQUIRED_VARS TIRPC_LIBRARIES TIRPC_INCLUDE_DIRS
    VERSION_VAR TIRPC_VERSION
)

mark_as_advanced(TIRPC_INCLUDE_DIRS TIRPC_LIBRARIES)

and add

list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/modules)

to apbs/externals/fetk/maloc/CMakeLists.txt and use something like find_package(TIRPC) instead of directly trying to find rpc/rpc.h?

kozlac commented 4 years ago

Hello @dvdesolve! Thanks for providing the cmake find_pacakage(TIRPC)! We have seen this issue mainly in Fedora based systems. Also, I will look into why there are no rules to copy the missing binaries and libraries during installation. We are in the process of refactoring a lot of the code and will add these to the list of coming changes. Thank you!

sobolevnrm commented 4 years ago

@kozlac -- have you made any progress with this? @intendo - given that you're looking into the cmake setup, could you take over?

intendo commented 3 years ago

This appears to still be a problem especially with building shared libraries. The shared libraries do not get installed. The static libraries for the external projects do get installed. This seems backwards. Hopefully @ashermancinelli can help me figure this one out so we can get new releases built.

nsoblath commented 2 years ago

I believe this is now outdated, but please raise a new issue if there are still problems.