Apbsplugin

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

There is a nice tutorial on the APBS homepage: [1]
For further help, there is a mailing list [2] with the corresponding archive [3]

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
#load 3ig7.pdb, 3IG7
create cdk2, 3IG7 and polymer
create EFP, 3IG7 and organic and not resn ACE
delete 3IG7

hide everything, all
#h_add cdk2
#h_add EFP
show_as cartoon, cdk2
show_as sticks, EFP
util.cbay EFP

### If modules does not like funny names of atoms, we can rename them. Uncomment these lines, if it is a problem
#python
#Ligand_prop = []
#cmd.iterate("EFP", "Ligand_prop.append((resi, resn, name, elem, ID))")
#for resi, resn, name, elem, ID in Ligand_prop:
#    print("resi %s, resn %s, name %s, elem %s, ID %s"%(resi, resn, name, elem, ID))
#    cmd.alter('%s and id %s'%(resn,ID),'name=%s%s%s'%('"',elem,'"'))
## To see the change, we rewrite the list.
#Ligand_prop = []
#cmd.iterate("EFP", "Ligand_prop.append((resi, resn, name, elem, ID))")
#for resi, resn, name, elem, ID in Ligand_prop:
#    print("resi %s, resn %s, name %s, elem %s, ID %s"%(resi, resn, name, elem, ID))
#python end

select flexible, byres cdk2 within 3.5 of EFP
show sticks, flexible
util.cbag flexible
disable flexible
zoom cdk2

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

Click in Selection to use, and write cdk2. 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.