VMD-L Mailing List

From: jcorradi_at_criba.edu.ar
Date: Tue May 15 2012 - 08:28:28 CDT

Thank you axel for your response, iīve been trying to get the pqr file
from the pdb2pqr web server. I have the pdb and Mol2 files but i
always recieve this error message:
            Status
            Message: error
            Run time: -1 seconds
            Current time: Tue May 15 05:56:42 2012
            There was an error with your query request. This page will
not refresh.

I donīt know which could be the problem.
thanks for any suggestion
jere

> 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.
>

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