Re: [Apbs-users] surface electrostatic potentials

[Nathan B. <ba...@bi...>]

Hi Joao --

You can control the pH of your calculation if you generate the PQR  
files with PDB2PQR (http://pdb2pqr.sf.net/) and use those generated  
PQR files in your APBS calculation.

More details about using externally-generated PQR files in PyMOL can  
be found at http://apbs.wustl.edu/MediaWiki/index.php/APBS_electrostatics_in_PyMOL

Please let us know if you have any questions.

-- Nathan

On Nov 5, 2009, at 10:56 AM, Joao Dias wrote:

> Dear Apbs users,
> I am using APBS through PYMOL to calculate protein surface
> electrostatic potentials and then visualize them in PYMOL.
> Are the surface electrostatic potentials calculated at pH 7?
> Is it possible to calculate the same surface electrostatic potentials
> at a different pH, for example pH 5.5?
>
> All the best,
> Joao
>
>
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—
Nathan Baker (ba...@bi...)
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis
Web: http://bakergroup.wustl.edu/