VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 01 2011 - 12:25:04 CDT

On Wed, Jun 1, 2011 at 12:48 PM, Raul Araya <arayasecchi_at_gmail.com> wrote:
> Dear VMD users:
>
> I have the psf and dcd trajectory of a molecular system (protein + POPC +
> water + ions). I want to use the PMEpot plugin for the calculation of the
> electrostatic potential of the system. But I have some doubts: The charges
> used for the calculation will be those on the psf file or I have to input

the charges used will be those that are internally stored in VMD.
if you read in a .psf file, the charges in there is what is being used.

> them (using the "guess atomic charges from charrmm parameter" option, or

the guess option will try to match the atoms types with force field data
from charmm. this is using the engine in the apbsrun plugin.

> placing the charges in the beta field of the pdb of the system (using
> PDB2PQR for example?)

no.

axel.

>
> Thanks.
>
>
>
> Raúl Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> PhD Student (Biotechnology Program. UNAB, Chile)
> Computational Biology Lab (DLab)
> Center for Mathematical Modeling (CMM)
> Facultad de Ciencias Físicas y Matemáticas.
> Universidad de Chile.
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.