VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 15 2012 - 00:41:56 CDT

On Sun, May 13, 2012 at 11:00 PM, <jcorradi_at_criba.edu.ar> wrote:
> Hi everybody, i would like to analyze electrostatic potentials for a goup of
> ligands like serotonin, nicotin, and others. I“ve found the APBS tutorial
> from www.poissonboltzmann.org but i don“t know how to run the calculations
> for these ligands i mentioned... i believe it could be possible, am i right?
> or is it only for peptides?

APBS doesn't care what kind of molecule you have.
all it does is solving the poisson-boltzman equation
numerically and for that it needs a representation of
the charge distribution inside those molecules.

those are represented with pqr files. check out this link:
http://www.poissonboltzmann.org/pdb2pqr/

...and have a closer look at the detailed documentation
for APBS and its tutorials.

axel.

> thank you in advance
> Jere
>
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-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.