From: Raul Araya (
Date: Wed Jun 01 2011 - 11:48:07 CDT

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
them (using the "guess atomic charges from charrmm parameter" option, or
placing the charges in the beta field of the pdb of the system (using
PDB2PQR for example?)


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.