APBS

2008-04-27T01:32:01Z

Macdojme: /* Gentoo */

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ 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 kbT/ec) in the molecular display window (as with the image to the right). See [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page] 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 [http://pdb2pqr.sourceforge.net/ 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 [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''

==Required Dependencies==
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.

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===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed.
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch 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

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 [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].

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===Installing the Dependencies on Linux===

====From Scratch====
Note that this tutorial assumes you're using the bash shell and have root privileges
<OL><LI>
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) 
<LI>Set up some environment variables & directories (temporary for building)
<pre>
$ 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}
</pre></LI>
<LI>Unpack the source packages
<pre>
$ cd ${FETK_SRC}
$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -</pre>
</LI>
<LI>Compile MALOC
<pre>
$ cd ${FETK_SRC}/maloc
$ ./configure --prefix=${FETK_PREFIX}</pre>
If everything went well, then
<pre>$ make; make install</pre></LI>
<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
<LI>Now on to compiling APBS itself
<pre>
$ cd ${FETK_SRC}/apbs-0.4.0
$ ./configure --prefix=${FETK_PREFIX}</pre>
If all goes well:
<pre>$ make all; make install</pre></LI>
<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
<LI> There will now be an APBS binary at
<pre>/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</pre></LI>
<LI> Make appropriate links
<pre>
$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
</pre></LI>
<LI> Get rid of /<building directory dir>/temp_apbs
<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
<LI> Rock and or Roll.
</OL>

====Pre-Packaged====
=====RPMs=====

A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ 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 [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux 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

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==Further contributions and edits are needed.==

PyMOL Wiki - User contributions [en]

APBS