Hello Dr. Baker,

I want to run linearized Poisson-Boltzman calculations of electrostatic potential mapped only to the atoms of interest. In my *.in file, I have the "comps" flag present for the "calcEnergy" command, but I was wondering if there was a way to limit the number of atoms that are written to the output file.

We have APBS installed on local machines running Linux, so I could probably write a script that can extract the relevant information. I was just curious if this function was supported in APBS, maybe through the "Print" or "Write" commands?

Thanks!
Sean


Nathan Baker wrote:
Hi Sean --

Can you say more about what types of calculations you're thinking of?  Are these just potential visualization calculations or more complicated energy calculations?

Thanks,

Nathan

On Jun 13, 2009, at 12:58 PM, Sean Barron wrote:

Hello everyone,

I am completely new to APBS, and I was wondering if there a way to limit the electrostatic calculations to specific residues within a given protein? I have introduced point mutations in silico and only need data from those positions.

Any help would be greatly appreciated.

Cheers,
Sean
-----------
Sean Barron
Curriculum in Neurobiology & Dept. of Pharmacology
University of North Carolina at Chapel Hill 
sbarron@med.unc.edu
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Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis









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