electrostatics / apbs Goto Github PK

Software for biomolecular electrostatics and solvation calculations

Home Page: http://www.poissonboltzmann.org/

License: Other

Shell 0.62% CMake 1.24% HTML 0.01% Makefile 1.75% Fortran 2.56% Rich Text Format 2.60% C 66.35% C++ 0.66% Awk 0.35% Python 10.65% sed 0.16% Io 0.33% TeX 1.78% MATLAB 10.53% SWIG 0.41%

chemistry bioinformatics biophysics hacktoberfest

apbs's Introduction

APBS - Adaptive Poisson-Boltzmann Solver

This repository contains the APBS software.

For more information about APBS, please see

Home page: http://www.poissonboltzmann.org/
Documentation: http://apbs.readthedocs.io

apbs's People

Contributors

Stargazers

Watchers

apbs's Issues

Dielectric interface definitions

Would it be useful to include something like the attached somewhere in the APBS documentation?
Dielectric coefficient model families.pdf

Implement other boundary conditions for Geometric Flow

@sobolevnrm, only "mdh" is implemented, adding "zero" would be easy to add. What other boundary conditions do you want to see implemented?
Should use APBS's boundary condition code for this instead of implementing our own from scratch.

Setup build system to produce static libraries given a CMake option

Linking issues

Describe the bug
3.0.0 release can't be built because of linking issues. I'm getting the following errors:

[ 69%] Linking C shared library ../../lib/libapbs_pmgc.so
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collect2: error: ld returned 1 exit status
make[2]: *** [src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make:358: lib/libapbs_pmgc.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:1383: src/pmgc/CMakeFiles/apbs_pmgc.dir/all] Error 2
make: *** [Makefile:182: all] Error 2

To Reproduce
Steps to reproduce the behavior:

Download all necessary submodules
Run CMake and make with:

    cmake \
        -DCMAKE_INSTALL_PREFIX=/usr \
        -DCMAKE_BUILD_TYPE=Release \
        -DENABLE_GEOFLOW=ON \
        -DENABLE_BEM=OFF \
        -DENABLE_FETK=ON \
        -DENABLE_OPENMP=ON \
        -DENABLE_PBAM=ON \
        -DENABLE_PBSAM=ON \
        -DENABLE_PYTHON=ON \
        -DENABLE_TESTS=OFF \
        -DBUILD_SHARED_LIBS=ON \
        -DBUILD_DOC=OFF \
        ..

    make

See error

Expected behavior
Clean and nice compilation

Desktop (please complete the following information):

OS: Arch Linux 64 bit

Documentation for APBS geometric flow functionality

We need some documentation for the geometric flow functionality in APBS.

Replace data in Markdown with CSV

Replace the data in apbs/examples/*/README.md with one or more CSV tables to facilitate testing and generating data for new releases.

Add LPBE/NPBE support to geometric flow or remove the ion and lpbe keywords.

Need to remove ion and lpbe keywords from geoflow

Please strip share/apbs/tools/bin/* executables

====> Running Q/A tests (stage-qa)
Warning: 'share/apbs/tools/bin/uhbd_asc2bin' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/dx2mol' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/dx2uhbd' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/tensor2dx' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/analysis' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/similarity' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/del2dx' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/dxmath' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/benchmark' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/smooth' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/multivalue' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/value' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/mergedx2' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/mgmesh' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/mergedx' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'share/apbs/tools/bin/coulomb' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}

installation issue with CUDA

Describe the bug
Fails to install from conda with no real conflicts and with a strange error message.

To Reproduce
Steps to reproduce the behavior:

$conda create -n myenv python=3.6 && conda activate myenv
$conda install -c electrostatics apbs

Output in format: Requested package -> Available versions
The following specifications were found to be incompatible with your CUDA driver:

  - feature:/linux-64::__cuda==10.2=0

Your installed CUDA driver is: 10.2

Expected behavior
clear installation

Desktop (please complete the following information):

OS: Fedora 30, Ununtu 18.04

Additional context
The problem looks similar to this. There, the problem was in how the conda package was built and the fix came from the author himself.

Fix test coverage and integrate with Travis CI

Make PyPI package for apbs

geoflow box size effect bug

From a user (fortran code):

I think I figured out why the surface area and non-polar solvation energy kept increasing with increase in box size. The problem can be found in the time-integration routine (of the original geometric flow code) for the solvent characteristic S function: subroutine UPWINDING in surfconcz.f90.

The equation for the time evolution of the S function has the gradient vector of the S function and its magnitude appearing on its right hand side.

In the time-integration routine, a small number (effectively a value of 1e-3) was always added to the magnitude of the gradient S vector at each grid point of the solvent-occupied region. I think the reason why Zhan did this was to avoid the division by zero if the gradient S vector components took zero values , as one of the terms in the equation has the magnitude of the gradient S vector appearing in the denominator. But, there is another term that multiplies the magnitude with the “generalized” potential function V; this term should go to zero when the actual magnitude of gradient S vector is zero; but because of the small non-zero value, this term does not go to zero, which is the source of the error that we see in the surface area and non-polar solvation energy calculations when the box size was increased.

Try running the fortran code with different values for EXTVALUE (in fort.12): 4 , 6, 8,10.

Does APBS 'make test' work on all supported systems?

Standard platform for testing build system for APBS

PBAM Failing CTest

PBAM is failing the CTests.

unable to calculate surface potential at different pH values of whole capsid

Hello everyone,

I'm new to the party and have some issues regarding calculating my surface potential and hope to find a solution for my problem.

I try to calculate the surface potential at different pH values with the following arguments for the pdb2pqr command line in APBS tools 2.1 in Pymol (e.g. pH 2): --with-ph=2.0 --ph-calc-method=propka

When I want to show the surface potential only the asymmetric unit is calculated at pH 2.0 and the other parts the protein container surface seem to be calculated at pH 7.0 - so at standard pH value.
Why is only a part calculated at pH 2.0 and the other residues at standard? What do I have to change? I created the capsid through generating symmetry mates and saved it in one PDB file as one object. Also if i want to use the web server, only the asymmetric unit is calculated for the given pH value.

Thanks a lot in advance and stay healthy.

add "glen" and "dime" parameters to geometric flow domain initialization

Currently, the size of the domain in geoflow (AKA "glen" in APBS) is calculated by taking a bounding box around the atoms, padded by "p_extvalue" and divided by grid (dcel) size. The "domainInitialization" method in GeometricFlow.cpp needs to be rewritten (and tested) to handle domain sizes specified by the user.

Also add "dime" (the number of grid points per processor for grid-based discretization) - glen, grid, and dime: the user should be able to specify two of these with the remainder calculated by the formula: glen = grid * (dime – 1)

Replace SWIG with something from the last decade

Priority is to replace IO functionality (eg NOSH) first and work towards the more substantial kernels as needed.

The gamma keyword uses two different sets of units...

... in APOLAR and ELEC geoflow. We need to reconcile these.

Add units to geoflow input/output

Hello,
I think there is still ambiguity in APBS 3.0.0 (that does not output energy units in the geoflow computation) and the definition of the keywords on the website. Are gamma and press given in kcal or kJ? Thank you very much for writing this code. I'm very grateful for it.

Originally posted by @sozenoid in Electrostatics/apbs-pdb2pqr#29 (comment)

Restore ability to link APBS with TINKER

We used to be able to link APBS with TINKER (http://dasher.wustl.edu/ffe/) which allowed us to do cool things like this: http://www.ncbi.nlm.nih.gov/pubmed/17411115

Unfortunately, after all of the build system upgrades, this linkage no longer works.

Problems Compiling APBS 3.0

Hello,

I am trying to compile APBS 3.0 under Centos 7 using cmake 3.17. The process simply dies with a message that does not tell me much about what is happening.

This is what I did:

Downloaded the source code for Linux
Expanded the tgz file
Went into the apbs directory
Tried to compile with cmake path_to_apbs_directory

At this point the process dies with a message "Configuring incomplete, errors occurred!"

I did the compilation again using the verbose mode for cmake to see if I obtained more information. Something that I noticed is that I get the following error in the cmake output:
CMake Error at CMakeLists.txt:310 (add_subdirectory):
add_subdirectory given source
"/home/lmurga/APBS_3/Source/apbs-3.0.0/apbs/externals/fetk/maloc" which is
not an existing directory.

There is fetk directory in the apbs tree but it is empty which maybe explain the error.

Do I need to download additional files? If so, from where.
Are all the options like FETK, PB-AM, etc. activated by default?

Please advise. Thanks for your help

Pedro

I am attaching the output of the cmake command and the CMakeOutput.log

cmake.out.txt
CMakeOutput.log.txt

Update www.poissonboltzmann.org for standalone apbs repo

APBS 1.5 binary installed, doesn't run multiple tthreads!

I recently download the binary from the 1.5 version and after fixing the LD_LIBRARY_PATH, I was able to run a case. However it doesn't run in multiple threads.
The same input file, runs in multiple thread in a 1.4.1 version I had installed. I tried to install the 1.5 binary in different machines and I always get the same problem. It only runs in 1 thread.

Any ideas on what can be causing this?

For the record, I have 1 processor with 4 physical cores (hyperthreading 8) . The input file looks like:

read 
    mol pqr built_parse.pqr
end

# LYSOZYME SOLVATION ENERGY -- SOLVATED STATE
elec name lys-solv
    mg-manual
    dime 257 161 257  
    glen 50 40 50 
#    glen 69.43 61.38 77.82
    gcent mol 1
    mol 1
    lpbe
    bcfl mdh
    ion charge 1 conc 0.15 radius 2.0                
    ion charge -1 conc 0.15 radius 2.0      
    pdie 4.0
    sdie 80.00
    chgm spl2
    srfm mol
    srad 1.4
    swin 0.3
	sdens 50.0
    temp 300.00
    calcenergy total
    calcforce no            
end

# LYSOZYME SOLVATION ENERGY -- REFERENCE STATE
elec name lys-ref
    mg-manual
    dime 257 161 257 
    glen 50 40 50 
#    glen 69.43 61.38 77.82
    gcent mol 1
    mol 1
    lpbe
    bcfl mdh
    ion charge 1 conc 0.00 radius 2.0                
    ion charge -1 conc 0.00 radius 2.0 
    pdie 4.0
    sdie 4.00
    chgm spl2
    srfm mol
    srad 1.4
    swin 0.3      
	sdens 50.0
    temp 300.00
    calcenergy total
    calcforce no
end

# Lysozyme solvation energy
print elecEnergy lys-solv - lys-ref end

quit

Create a "big memory" test case

Basically, I'd like to have test cases that demonstrate that we can allocate memory up to the limit where signed integers stop working on 32-bit and 64-bit systems.

Remove references to PDB2PQR from docs and config files

Python Porting

Problem Description

Much of the current C/C++ code is difficult to maintain as expressed by other teammembers. Not many domain experts are proficient enough in this codebase to contribute as proficiently as they otherwise could (as I was informed by @intendo) were the codebase in Python.

Describe the solution you'd like

I think we should take a multi-phasic approach to porting this code to Python, in order to work only in the smallest testable chunks.

Step 1: Data Structures

Port the smallest data structures that are used frequently (as determined by @intendo's impressive callgraph work).

Step 2: The Smallest Chunks

Port smaller routines/methods that operate on the smaller data structures

Add as many tests as are reasonable to add after porting each method
Grab a data-dump of the input/output of the C/C++ kernels to use as unit tests for the Python implementations to ensure that the refactor correctly replicates the old kernels
heavily document the apparent responsibilities of all routines/data structures that are ported

Step 3: Port More Complicated Routines

Write unit tests for larger routines/methods in the same way that the smaller routines/methods were tested
The smaller methods are already tested at this point, so we know that as long as we compose the methods in the same way, the larger tests will also perform the same way. These tests will likely not be as long as the methods themselves as a result.

Step 4: Reevaluation

Re-evaluate the algorithms and data structures used. At this point, we would have tests for the highest-level routines that are used in the codebase. We could therefore test a new implementation in the same way, with more involvement from domain experts that could more meaningfully contribute to the project. We would therefore have full assurance that our refactor would be consistent with the old implementation.

We would also be able to swap out different python implementations for the larger kernels since we would have tests all the way down to the smallest chunks. We would know exactly where/when our new implementation differed from the old.

Describe alternatives you've considered

Alternative 1

We could attempt to port over larger chunks of the at once, however I don't think this is the best route.
For example, in the directory apbs/src/routines.c we have the function solveMG, which is the most frequently called function out of all the profiled runs @intendo ran. This calls Vpmg_solve in another file, which performs many steps before calling Vmgdriv or Vnewdriv depending on the options. In yet another file, Vmgdriv then performs many more operations before calling Vmaxlev, Vmgsz, and Vmgdriv2, each of which take a massive number of parameters and operate on many of the same massive data structures.

In my opinion and experience, porting solveMG will only really be possible once we have tests for the smaller routines (Vmgdriv, Vmaxlev, etc), all the way down to the bottom.

NOTE: None of this is to disparage the original authors of this code - it was clearly written by talented engineers and domain experts. However, if we are to port (or interface) this to Python, I believe we will have to take this step by (well-tested) step.

Alternative 2

We could also keep the python bindings to this program relatively thin, in which case I think we ought to just generate some Python bindings through the cpython API and let users work with the API directly. However, from my understanding, other members of this project strongly prefer not to take this route.

Additional context

I have some small working examples of python implementations of Vatom and Vlist, along with unit tests to demonstrate. This is not the most thorough example, but nonetheless showcases how we might go about porting the program to python whilst keeping the organization of the code roughly the same until we have enough tests built up to really refactor substantial algorithms.

Progress

The following have Python implementations that are thoroughly tested (102 tests in total):

Chemistry
- Atom
- AtomList
- CellList
- Atom Complex Calculations (Vacc class)
  - atom_surface needs tests
  - accessable_outside_inflated_venderwalls_rad needs tests
Geometry
- Surface (partial)
- Sphere
  - spherical_distribution needs testing

Sparse Matrix CSR format for AtomList/CellList

Is your feature request related to a problem? Please describe.
The AtomList and CellList classes are essentially methods on top of a sparsely populated matrix, and the data access patterns for these classes could be vectorized by laying them out linearly in memory.

Describe the solution you'd like
We should store all data in AtomList and CellList in COO sparse matrix format, e.g.

class AtomList:
    def __init__(self, natoms: int):
        self.xs = np.array(natoms)
        self.ys = np.array(natoms)
        self.zs = np.array(natoms)
        self.vals = np.array(natoms)
        self.natoms = natoms

    def append(self, a: Atom) -> None:
        self.xs[self.natoms] = a.x
        self.ys[self.natoms] = a.y
        self.zs[self.natoms] = a.z
        self.vals[self.natoms] = a.val
        self.natoms += 1

In this case, we would be able to vectorize all operations that work on every value of the atom/cell list, and we could even take advantage of tensor libraries like pytorch or tensorflow and run some code on a GPU.

From what I've seen in the original APBS source, data is either laid out linearly and the index is calculated with an offset, or the data is stored as an array of fields which have the x/y/z coordinates and values as member variables. A sparse matrix format would provide us with similar algorithms at worst, and more vectorization at best. If the atoms usually densely populate the given space, I think we should then use a dense matrix instead.

What are your thoughts on this @sobolevnrm ?

CC @intendo

Check build instructions

@intendo can you please check https://github.com/Electrostatics/apbs/blob/nathan/docs/docs/getting/source.rst to see if it is correct?

MALOC modernization

It's no longer needed and takes extra effort to maintain.

Resolve unit confusion with geometric flow press keyword and the apolar press keyword.

Include installation documentation with code in main documentation

No in separate text, Markdown, Confluence, etc. files

python2->3 bug in psize.py

At line 175, a list is compared to an integer. This is ok to do in python2, but not 3:

To fix the issue, consider replacing line 175 with:

if any([val <= 0 for val in nsmall]):

make doesn't install everything

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 [email protected]
-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 [email protected]
-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 [email protected]
-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 [email protected]
-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 [email protected]
-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?

3.0.0 build instructions are confusing, do not work

Describe the bug
Unable to build 3.0.0 from source, I think because the build instructions are confusing and/or incomplete

To Reproduce

Attempt to follow instructions here:
https://apbs.readthedocs.io/en/latest/getting/source.html
It says to download "release" rather than do a git clone. There are two files for 3.0.0 that might plausibly fit that description (not counting different packaging), with no description of how they differ:

  https://github.com/Electrostatics/apbs/releases/download/v3.0.0/APBS-3.0.0_Source-Code.tar.gz
  https://github.com/Electrostatics/apbs/archive/v3.0.0.tar.gz

  cd /usr/common/src
  pversion=3.0.0
  package=apbs
  altpkg=APBS
  TOPDIR=/usr/common/modules/el8/x86_64/software/${package}/${pversion}-CentOS-vanilla
  wget https://github.com/Electrostatics/apbs-pdb2pqr/releases/download/v${altpkg}-${pversion}/${altpkg}-${pversion}_Source-Code.tar.gz
  gunzip -c ${altpkg}-${pversion}_Source-Code.tar.gz | tar -xf -
  /bin/rm ${altpkg}-${pversion}_Source-Code.tar.gz
  cd ${package}-${pversion}

The installation docs then say to do this after "git clone" (after first saying, do not do "git clone"). In any case
these do not work because git does not think this is a git repository. The steps following fail whether or not these
commands are issued, I don't think they do anything in the present case. I wonder though if the submodule update would have loaded in all the pieces which seem to cause problems further on, had this been a "git clone".

git submodule init
git submodule update

(Note, "extract" is from drm_tools on sourceforge, here it is just substituting the -rtss string wherever it finds the -rtds string.)

module load msms
module load nanoshaper
module load cmake
cp ../CMakeLists.txt ../CMakeLists.txt.dist
extract -in ../CMakeLists.txt.dist -out ../CMakeLists.txt \
  -rtds '_INSTALL_PATH ' -rtss "_INSTALL_PATH $TOPDIR/"
#this will hopefully fix both the "can't find Python.h" and link problems
cmake -DENABLE_GEOFLOW=ON -DENABLE_PBAM=ON \
 -DENABLE_BEM=ON -DENABLE_FETK=ON \
 -DENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON \
 -DGET_NanoShaper=ON . 2>&1 | tee cmake_oops.log

This fails with a variety of messages for the different ON packages, all in more or less this form (see attached also):

-- Building TABIPB
CMake Error at /usr/common/src/cmake-3.17.1/share/cmake-3.17/Modules/ExternalProject.cmake:2659 (message):
  No download info given for 'bem' and its source directory:

   /usr/common/src/apbs-3.0.0/apbs/externals/bem

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/common/src/cmake-3.17.1/share/cmake-3.17/Modules/ExternalProject.cmake:3267 (_ep_add_download_command)
  apbs/CMakeLists.txt:258 (ExternalProject_add)

This is CentOS 8. On 2020/04/21 an earlier version was built successfully with git clone like so:

  pversion=1.5 #determined after it was built
  package=apbs
  TOPDIR=/usr/common/modules/el8/x86_64/software/${package}/${pversion}-CentOS-vanilla
  cd /usr/common/src
  git clone https://github.com/Electrostatics/apbs-pdb2pqr.git
  cd apbs-pdb2pqr
  git submodule init
  git submodule update
  #needs MSMS or Nanoshaper. Both are now available as modules
  module load msms
  module load nanoshaper
  module load cmake #very recent release needed
  #Requires: OpenBLAS, installed on all nodes
  mkdir -p apbs/build
  cd apbs/build
  #edit /usr/common/src/apbs-pdb2pqr/apbs/src/routines.c to change all:
  #   for (int i=0
  #to
  #   int i; for (i=0
  #else it stops at:
  #  /usr/common/src/apbs-pdb2pqr/apbs/src/routines.c:5332:11: error: ?for? loop initial declarations are only allowed in C99 mode
  cp ../src/routines.c ../src/routines.c.dist
  extract -in ../src/routines.c.dist -out ../src/routines.c \
    -rtds 'for (int i = 0;' -rtss 'int i; for(i = 0;'
  cp ../CMakeLists.txt ../CMakeLists.txt.dist
  extract -in ../CMakeLists.txt.dist -out ../CMakeLists.txt \
    -rtds '_INSTALL_PATH ' -rtss "_INSTALL_PATH $TOPDIR/"

  #this will hopefully fix both the "can't find Python.h" and link problems
  cmake -DENABLE_GEOFLOW=ON -DENABLE_PBAM=ON \
   -DENABLE_BEM=ON -DENABLE_FETK=ON \
   -DENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON \
   -DGET_NanoShaper=ON ..
  make 2>&1 | tee build_2020_04_21.log

cmake_oops.log

Complete UQ parameter discussion

Someday I should finish https://github.com/Electrostatics/apbs-pdb2pqr/blob/master/doc/apbs/errors.rst

Units in geometric flow examples

Are the units in the geometric flow examples really kcal/mol/A^n? They should be kJ/mol/A^n.

Issues Building APBS

I'm on Mac OS 10.15.16 and am trying to build APBS from source (had no luck with the binary after trying for hours). I've followed the instructions on the website, but have not had any luck (specifically, if I clone the master branch I'm able to run cmake but then make crashes; if I try the specific release 3.0, cmake crashes).

If possible, I would really appreciate if someone could add some more detailed step by step instructions regarding how to build APBS from source. This is a great piece of software, but some more documentation would go a long way.

python3 compatibility?

Working on CentOS 8, which has "python2" and "python3" but not "python". Installing apbs was mostly OK, but pdb2pqr much less so, and the interaction between the two is not working at all well. Some of this is probably because python 2 was EOL'd on 1/12020 but apbs/pdb2pqr still uses it. Likely there is a "python" in there somewhere where only python2 or python3 is available.

But scons.py does not run with python3.

python3 scons/scons.py
  File "scons/scons.py", line 194
    print "  %s" % path
               ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("  %s" % path)?

apbs was built with (note, "extract" is from "drm_tools" on sourceforge, the here it is just doing substitions: rtss string2 replaces rtds string1.)

pversion=1.5 #determined after it was built
package=apbs
TOPDIR=/usr/common/modules/el8/x86_64/software/${package}/${pversion}-CentOS-vanilla
THELUA=/usr/common/modules/el8/x86_64/modules/all/${package}/${pversion}-CentOS-vanilla.lua
cp ../src/routines.c ../src/routines.c.dist
extract -in ../src/routines.c.dist -out ../src/routines.c \
  -rtds 'for (int i = 0;' -rtss 'int i; for(i = 0;'
cp ../CMakeLists.txt ../CMakeLists.txt.dist
extract -in ../CMakeLists.txt.dist -out ../CMakeLists.txt \
  -rtds '_INSTALL_PATH ' -rtss "_INSTALL_PATH $TOPDIR/"
git clone https://github.com/Electrostatics/apbs-pdb2pqr.git
cd apbs-pdb2pqr
git submodule init
git submodule update
module load msms
module load nanoshaper
module load cmake #very recent release needed
#Requires: OpenBLAS, installed on all nodes
mkdir -p apbs/build
cd apbs/build
cmake -DENABLE_GEOFLOW=ON -DENABLE_PBAM=ON \
   -DENABLE_BEM=ON -DENABLE_FETK=ON \
   -DENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON \
   -DGET_NanoShaper=ON ..
make 2>&1 | tee build_2020_04_21.log
#that worked!
make install 2>&1 | tee install_2020_04_21.log
#does NOT copy all the libraries
cp bem-prefix/src/bem-build/libTABIPBlib.so $TOPDIR/lib
(cd fetk/src/fetk-punc-build/src/aaa_lib/.libs; tar -cf - .) | (cd $TOPDIR/lib; tar -xf -)
(cd fetk/src/fetk-mc-build/src/aaa_lib/.libs; tar -cf - .) | (cd $TOPDIR/lib; tar -xf -)
(cd fetk/src/fetk-maloc-build/src/aaa_lib/.libs; tar -cf - .) | (cd $TOPDIR/lib; tar -xf -)
(cd fetk/src/fetk-gamer-build/src/aaa_lib/.libs; tar -cf - .) | (cd $TOPDIR/lib; tar -xf -)
/bin/rm $TOPDIR/lib/*.la
(cd fetk/lib; tar -cf - *.la) | (cd $TOPDIR/lib; tar -xf -)
module_generate_from_directory.sh \
   $package \
   $pversion \
   CentOS/vanilla \
   $TOPDIR \
   "Solve the equations of continuum electrostatics for large biomolecular assemblages." \
   "https://github.com/Electrostatics/apbs-pdb2pqr"

however, pdb2pqr downloaded that way would not build because html/server.html.in etc. are NOT in the download, So obtained and built pdb2pqr like this:

module load apbs
pversion=2.1.1
package=pdb2pqr
TOPDIR=/usr/common/modules/el8/x86_64/software/${package}/${pversion}-CentOS-vanilla
THELUA=/usr/common/modules/el8/x86_64/modules/all/${package}/${pversion}-CentOS-vanilla.lua
cd /usr/common/src
wget https://github.com/Electrostatics/${package}/archive/v${pversion}.tar.gz
gunzip -c v${pversion}.tar.gz | tar -xf - 
/bin/rm v${pversion}.tar.gz
cd ${package}-${pversion}
cp build_config.py build_config.py.dist
echo "" >> build_config.py.dist #fix missing newline
#NOTE: next also converts from \r\n to \n!  diff will show all lines!
extract -in build_config.py.dist -out build_config.py \
   -if '#PREFIX="~/pdb2pqr"' -fmt "PREFIX=\"$TOPDIR\""
#needed python2-devel RPM
python2 scons/scons.py 2>&1 | tee build_2020_07_28.log
python2 scons/scons.py local-test
#minor differences in values and in some cases atom order
#adv-test not a known target
python2 scons/scons.py complete-test  
#all SUCCESS, again minor differences as before
python2 scons/scons.py pdb2pka-test
#fails, needs numpy
#use python_devirtualizer to install, this just puts all the required
#libraries in one place and then makes links to it.
pdv2ctrl mkvenv forpdb2pqr
pdv2ctrl install forpdb2pqr "numpy networkx"
pdv2ctrl migrate forpdb2pqr /tmp/forpdb2pqr
export PYTHONPATH=/tmp/forpdb2pqr/lib/python2.7/site-packages
ls $PYTHONPATH
  decorator-4.4.2.dist-info  easy_install.py         numpy                   pip-20.1.1.dist-info   setuptools                    _virtualenv.pth  wheel
decorator.py               networkx                numpy-1.16.6.dist-info  pip-20.1.1.virtualenv  setuptools-44.1.1.dist-info   _virtualenv.py   wheel-0.34.2.dist-info
decorator.pyc              networkx-2.2.dist-info  pip                     pkg_resources          setuptools-44.1.1.virtualenv  _virtualenv.pyc  wheel-0.34.2.virtualenv
python2 scons/scons.py pdb2pka-test
#fails, some problem with apbs not being set up for python

it was unhappy and emitted these messages:

Missing libraries for interfacing with APBS

You need to build APBS with Python support using the CMake variable -DENABLE_PYTHON=ON.

There is nothing in the dynamic libraries in apbs which appears to be python related:

ldd `which apbs` | grep -i py
#nothing
ldd `which apbs` | grep -i libapbs
        libapbs_mg.so => /usr/common/modules/el8/x86_64/software/apbs/1.5-CentOS-vanilla/lib/libapbs_mg.so (0x00007f6888c57000)
        libapbs_fem.so => /usr/common/modules/el8/x86_64/software/apbs/1.5-CentOS-vanilla/lib/libapbs_fem.so (0x00007f6888a44000)
        libapbs_routines.so => /usr/common/modules/el8/x86_64/software/apbs/1.5-CentOS-vanilla/lib/libapbs_routines.so (0x00007f688882b000)
        libapbs_generic.so => /usr/common/modules/el8/x86_64/software/apbs/1.5-CentOS-vanilla/lib/libapbs_generic.so (0x00007f68885f8000)
        libapbs_pmgc.so => /usr/common/modules/el8/x86_64/software/apbs/1.5-CentOS-vanilla/lib/libapbs_pmgc.so (0x00007f68883c9000)

In short, this is not installing/working at all well (on CentOS 8), and at least some of the problem is that it is still tied to the older python language.

Convert input format to YAML and front-end to Python

Allow better integration with other codes.
Support more robust input file parsing

PB-SAM surf = usemesh
PB-SAM grid2d = write
PB-SAM dx = write (or read)
PB-SAM exp could be replaced with generalized version of APBS read
PB-SAM diff command ordering could be replaced with use of mol id

Single Cmake build/test system for APBS/PDB2PQR with Travis CI integration

Modernize documentation on RTD

It would be great to move the relevant APBS documentation to Sphinx for support on RTD. This probably has (at least) two parts:

@sobolevnrm can work on migrating the existing documentation from https://github.com/Electrostatics/apbs-pdb2pqr/tree/master/doc
@intendo would you be willing to look at solutions like https://devblogs.microsoft.com/cppblog/clear-functional-c-documentation-with-sphinx-breathe-doxygen-cmake/ to support the C/C++ portion of the API documentation?

The tools/multivalue utility (https://github.com/Electrostatics/apbs-pdb2pqr/blob/master/apbs/tools/mesh/multivalue.c) needs some --help (@keith923) and web (@ibloss) documentation. This could be as simple as cutting/pasting the comments in the file header into a string in the code and a new MarkDown documentation file for the web.

This was issue APBS-76 in JIRA.

Document Windows build process for APBS/PDB2PQR

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