APBS

Pre-release version

There's a pre-release version available on my user page. Please test it out and let me know if it works for you: --michael 03:04, 29 January 2010 (UTC)

Introduction

APBS-generated electrostatic surface displayed in PyMOL

APBS, the Adaptive Poisson-Boltzmann Solver, is a freely available macromolecular electrostatics calculation program released under the GPL. It is a cost-effective but uncompromised alternative to GRASP, and it can be used within pymol. Pymol can display the results of the calculations as an electrostatic potential molecular surface.

PyMol currently supports the APBS plugin written by Michael Lerner. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units <math>K_bT/e_c</math>) in the molecular display window (as with the image to the right). See the APBS wiki for more details, including instructions on how to download, install and use the plugin.

Nucleic acids may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the main menu to read the pqr file you externally generated.

Required Dependencies

APBS and its dependencies like pdb2pqr and maloc are freely available under the GPL. The author of the software however asks that users register with him to aid him in obtaining grant funding.

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Installing the Dependencies on OS X

1. First, register your use of the software. This will keep everyone happy.
2. Second, if you don't already have the fink package management system, now is a good time to get it. Here is a quick-start set of instructions for getting X-windows, compilers, and fink all installed.
3. Once you are up and going, activate the unstable branch in fink, and then issue the commands

fink self-update
fink install apbs

or if you want to use the multi-processor version, issue

fink self-update
fink install apbs-mpi-openmpi

Then install the X-windows based version of pymol using the command

fink install pymol-py25

Note that the fink version of pymol already has the latest version of the APBS plugin. You are set to go!

Further details, as well as screen shots, are given elsewhere in this wiki.

Installing the Dependencies on Linux

From Scratch

Note that this tutorial assumes you're using the bash shell and have root privileges

1. Obtain APBS and MALOC from...
   APBS = http://apbs.sourceforge.net (currently 0.4)
   MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2)
   
2. Set up some environment variables & directories (temporary for building)

   $ export FETK_SRC=/<building directory>/temp_apbs
   $ export FETK_PREFIX=/usr/local/apbs-0.4.0  (or wherever you want it to live)
   $ export FETK_INCLUDE=${FETK_PREFIX}/include
   $ export FETK_LIBRARY=${FETK_PREFIX}/lib
   $ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
   

3. Unpack the source packages

   $ cd ${FETK_SRC}
   $ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
   $ gzip -dc apbs-0.4.0.tar.gz | tar xvf -
   

4. Compile MALOC

   $ cd ${FETK_SRC}/maloc
   $ ./configure --prefix=${FETK_PREFIX}
   

   If everything went well, then

   $ make; make install
   

5. Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.
6. Now on to compiling APBS itself

   $ cd ${FETK_SRC}/apbs-0.4.0
   $ ./configure --prefix=${FETK_PREFIX}
   

   If all goes well:

   $ make all; make install
   

7. No time for coffee. Takes about 5 minutes on that fast computer.
8. There will now be an APBS binary at

   /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs
   

9. Make appropriate links

   $ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
   

10. Get rid of /<building directory dir>/temp_apbs
11. Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
12. Rock and or Roll.

Pre-Packaged

RPMs

A variety of RPMs are available from the APBS downloads website. Again, please register your use of the software if you have not yet done so.

Debian packages

For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program alien, and then install the newly generated debian package with the command

sudo dpkg -i apbs*.deb

Gentoo

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:

echo sci-chemistry/pdb2pqr >> /etc/portage/package.keywords
echo sci-chemistry/apbs >> /etc/portage/package.keywords
emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr

Troubleshooting

• If the B-factor is <math>\geq 100,</math> then APBS doesn't properly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100.

  alter all, b=min(b,99.9)
  

  The problem stems from how to parse a PDB file. The PDB file originally was written when most people used FORTRAN programs, and so the file format was specified by columns, not by the more modern comma separated value format we tend to prefer today. For the latest on the PDB format see the new PDB format docs.
• APBS has problems, sometimes, in reading atoms with alternate conformations. You can remove the alternate locations with a simple script removeAlt.
• ObjectMapLoadDXFile-Error: as of this writing (9-23-2008) a known problem exists, and the Baker lab is working on it. It is typically caused by the use of directories with spaces in their names under Windows.

Problems with the bundled version of APBS

There is an issue with the freemol version of APBS shipped with PyMOL 1.2r2 for OS X.

Leopard and Snow Leopard (10.5 and 10.6)

There are three fairly easy ways to resolve it

1. Download and install the most recent (post Dec. 1 2009) version of APBS from [1]. Then copy the apbs binary into the freemol directory (mv it to /Applications/PyMOLX11Hybrid.app/pymol/freemol/bin/apbs.exe, overwriting the version that comes installed with PyMOL).

2. Download File:Libgfortran.3.dylib.bz2, unzip it ("bunzip2 libgfortran.3.dylib.gz2") and move it to /usr/local/lib ("mv libgfortran.3.dylib /usr/local/lib" ... on some machines, you may need "sudo mv libgfortran.3.dylib /usr/local/lib").

bunzip2 libgfortran.3.dylib.gz2
mv libgfortran.3.dylib /usr/local/lib

3. Use macports to install gcc 4.4.2 and link the appropriate library ("ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib" ... on some machines, you may need "sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib").

ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib

If you're curious, the problem is that APBS is dynamically linked, but Apple does not provide FORTRAN libraries.

The version of libgfortran above is covered by the GNU General Public License (GPL). A copy of the GPL may be found at [2], and the source may be obtained from MacPorts ([3]).

Tiger (10.4)

You'll need to install APBS yourself via MacPorts or via fink. Fink instructions may be found on the APBS page. Installation via MacPorts requires first installing MacPorts from [4] and then typing

sudo port install apbs

from the command line. This process could easily take several hours on an older machine, as MacPorts will recompile gcc, gfortran, and several other packages along the way.