Difference between revisions of "APBS"

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== Introduction ==
 
 
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
 
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
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[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.
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[http://www.poissonboltzmann.org/ APBS], the Adaptive Poisson-Boltzmann Solver, is a
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[http://www.oreilly.com/openbook/freedom/ freely]
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available macromolecular electrostatics calculation program released under a
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[http://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/license.html BSD license].
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PyMOL can display the results of the calculations as an electrostatic potential molecular surface.
  
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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 k<sub>b</sub>T/e<sub>c</sub>) 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.
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== APBS Plugins for PyMOL ==
  
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'''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.'''
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* [[APBS Electrostatics Plugin]], included in [https://pymol.org/ Incentive PyMOL 2.0]
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* [[apbsplugin|APBS Tools 2.1]], based on the original version by [[User:Mglerner|Michael Lerner]].
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Both plugins make it possible to run APBS from within PyMOL, and then display
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the results as a color-coded electrostatic surface (units <math>K_bT/e_c</math>)
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in the molecular display window (as with the image to the right).
  
 
==Required Dependencies==
 
==Required Dependencies==
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[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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----
 
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===Installing the Dependencies on OS X===
 
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#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software.  This will keep everyone happy.
 
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#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.
 
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#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
 
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fink self-update
 
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fink install apbs
 
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or if you want to use the multi-processor version, issue
 
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fink self-update
 
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fink install apbs
 
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Then install the X-windows based version of pymol using the command
 
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fink install pymol-py25
 
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Note that the fink version of pymol '''already has''' the latest version of the APBS plugin.  You are set to go!
 
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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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----
 
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===Installing the Dependencies on Linux===
 
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====From Scratch====
 
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Note that this tutorial assumes you're using the bash shell and have root privileges
 
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<OL><LI>
 
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Obtain APBS and MALOC from...<br>
 
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APBS = http://apbs.sourceforge.net (currently 0.4)<br>
 
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MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2)<BR>
 
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<LI>Set up some environment variables & directories (temporary for building)
 
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<pre>
 
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$ export FETK_SRC=/<building directory>/temp_apbs
 
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$ export FETK_PREFIX=/usr/local/apbs-0.4.0  (or wherever you want it to live)
 
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$ export FETK_INCLUDE=${FETK_PREFIX}/include
 
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$ export FETK_LIBRARY=${FETK_PREFIX}/lib
 
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$ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
 
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</pre></LI>
 
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<LI>Unpack the source packages
 
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<pre>
 
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$ cd ${FETK_SRC}
 
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$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
 
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$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -</pre>
 
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</LI>
 
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<LI>Compile MALOC
 
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<pre>
 
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$ cd ${FETK_SRC}/maloc
 
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$ ./configure --prefix=${FETK_PREFIX}</pre>
 
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If everything went well, then
 
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<pre>$ make; make install</pre></LI>
 
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<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
 
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<LI>Now on to compiling APBS itself
 
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<pre>
 
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$ cd ${FETK_SRC}/apbs-0.4.0
 
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$ ./configure --prefix=${FETK_PREFIX}</pre>
 
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If all goes well:
 
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<pre>$ make all; make install</pre></LI>
 
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<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
 
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<LI> There will now be an APBS binary at
 
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<pre>/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</pre></LI>
 
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<LI> Make appropriate links
 
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<pre>
 
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$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
 
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</pre></LI>
 
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<LI> Get rid of /<building directory dir>/temp_apbs
 
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<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
 
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<LI> Rock and or Roll.
 
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</OL>
 
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====Pre-Packaged====
 
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=====RPMs=====
 
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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.
 
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=====Debian packages=====
 
  
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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
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The plugins require '''apbs''' and '''pdb2pqr'''.
  
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sudo dpkg -i apbs*.deb
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* [https://pymol.org Incentive PyMOL] ships preconfigured with apbs and pdb2pqr
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* [https://github.com/Electrostatics/apbs-pdb2pqr/releases Official release downloads] for all platforms
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* Precompiled packages are also available in Ubuntu, Debian, Gentoo, [https://www.macports.org/ MacPorts], [http://www.finkproject.org/ Fink], and many other Unix-like distributions. Example for installation on Ubuntu:
  
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=====Gentoo=====
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apt-get install apbs pdb2pqr
  
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You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:
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After all components are installed, open the plugin and browse for apbs and pdb2pqr on the "Program Locations" tab (if they haven't been found automatically).
  
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  echo sci-chemistry/pdb2pqr >> /etc/portage/package.keywords
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== Troubleshooting ==
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* ''(this might be outdated information):'' 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. <source lang="python">alter all, b=min(b,99.9)</source>  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 [http://www.wwpdb.org/docs.html new PDB format docs].
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* APBS has problems, sometimes, in reading atoms with '''alternate conformations'''.  You can remove the alternate locations with a simple script [[removeAlt]].
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* For pdb2pqr, '''RNA''' resdiue names must be RA, RC, RG, and RU.<source lang="python">alter polymer & resn A+C+G+U, resn = "R" + resn</source>
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* Incomplete Residues: Some truncated PDB files include a single backbone atom of the next residue, e.g. [https://www.rcsb.org/structure/2xwu 2xwu] chain B residue 954 atom N. '''pdb2pqr''' reports: ''Error encountered: Too few atoms present to reconstruct or cap residue LEU B 954 in structure!''. The easiest solution is to remove that atom:<source lang="python">remove /2xwu//B/954</source>
  
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echo sci-chemistry/apbs >> /etc/portage/package.keywords
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[[Image:Apbs_ex.png|thumb|right|300px|PyMOL visualizing two maps at once]]
  
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emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr
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==Using APBS==
  
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----
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See [[APBS Electrostatics Plugin]] and [[apbsplugin|APBS Tools2.1]].
  
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==Further contributions and edits are needed.==
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[[Category:Electrostatics]]
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[[Category:Biochemical_Properties]]
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[[Category:Plugins]]

Latest revision as of 15:05, 26 July 2018

APBS-generated electrostatic surface displayed in PyMOL

APBS, the Adaptive Poisson-Boltzmann Solver, is a freely available macromolecular electrostatics calculation program released under a BSD license. PyMOL can display the results of the calculations as an electrostatic potential molecular surface.

APBS Plugins for PyMOL

Both plugins make it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units ) in the molecular display window (as with the image to the right).

Required Dependencies

The plugins require apbs and pdb2pqr. 

apt-get install apbs pdb2pqr

After all components are installed, open the plugin and browse for apbs and pdb2pqr on the "Program Locations" tab (if they haven't been found automatically).

Troubleshooting

  • (this might be outdated information): If the B-factor is 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.
  • For pdb2pqr, RNA resdiue names must be RA, RC, RG, and RU.
    alter polymer & resn A+C+G+U, resn = "R" + resn
  • Incomplete Residues: Some truncated PDB files include a single backbone atom of the next residue, e.g. 2xwu chain B residue 954 atom N. pdb2pqr reports: Error encountered: Too few atoms present to reconstruct or cap residue LEU B 954 in structure!. The easiest solution is to remove that atom:
    remove /2xwu//B/954
PyMOL visualizing two maps at once

Using APBS

See APBS Electrostatics Plugin and APBS Tools2.1.

Retrieved from "http://pymolwiki.org/index.php?title=APBS&oldid=12790"