Difference between revisions of "Apbsplugin"

Revision as of 12:55, 6 December 2011

Software requirements

Register use of the software. This will the authors able to require funding for further development.
Register here, it takes 1 minutes: http://www.poissonboltzmann.org/apbs/downloads

Windows

Download APBS.msi from: http://sourceforge.net/projects/apbs/files/apbs/
MALOC?

Ubuntu

APBS are in the repository: http://packages.ubuntu.com/search?keywords=apbs
MALOC are in the repository: http://packages.ubuntu.com/search?keywords=libmaloc1

Compile yourself

If you really want, then see this section: APBS

Example 1 - Rename of funny atom names

Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7

reinitialize 
fetch 3IG7, async=0

Open the APBS Tool2.1... plugin. The executable should be found for itself:

Click tab Grid settings. In Calculate Grid Center by Selection, write EFP.
Try clicking Wired Box in top right, and then Show Box, Hide Box, Cylindric Box, Show Box.
Then push Select binding site. In PyMOL, write

show sticks, binding_site
cmd.disable("binding_site")
hide sticks, binding_site

Click tab Receptor. Mark cdk, and click Generate Receptor.
Click cdk2 to the "right", and see where the files are located.
Click tab Ligands. Mark EFP, and click EFP in the Ligand list. Here is the files stored. Click Generate Ligand
Click tab Docking, and click Run Vina. Wait 3-5 minutes, until Writing output ... done.
Click tab View poses, Browse to EFP.docked.pdbqt. Click Load, Show best 10. Experiment with "Display options, and click the candidates"
Congratulations, you did it!

Troubleshooting

See: APBS#Troubleshooting

References and LICENSES

APBS

When using the APBS, you are "obligated" to register your use of the software. This will the authors able to require funding for further development.
Register here, it takes 1 minutes: http://www.poissonboltzmann.org/apbs/downloads

Please acknowledge your use of APBS by citing:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. doi:10.1073/pnas.181342398

Please acknowledge your use of the Holst group software by citing:
M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993.
M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem. 16, 337-364, 1995.
For PMG (the multigrid solver):
M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics 15, 139-191, 2001. doi:10.1023/A:1014246117321
For FEtk (the finite element solver):
R. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Review 45, 291-323, 2003. doi:10.1137/S003614450342061

pdb2pqr

When using the pdb2pqr, you are "strongly encourage" to register your use of the software. This will the authors able to require funding for further development.
Register here, it takes 1 minutes: https://spreadsheets.google.com/viewform?hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA..

MALOC

Please acknowledge the use of MALOC and FETK by citing:
M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics, 15 (2001), pp. 139-191.

Copyright and Terms of Use:
GNU General Public License: http://www.gnu.org/copyleft/gpl.html

This version of MALOC is distributed under the following guidelines:
MALOC (Minimal Abstraction Layer for Object-oriented C) 
Copyright (C) 1994-2010 Michael Holst 

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. 

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. 

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

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 == 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. <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].
+See: [[APBS#Troubleshooting]]
-* 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.
 == References and LICENSES ==