VMD-L Mailing List

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Thu Jun 14 2012 - 10:02:58 CDT

Dear VMD users:

I have a psf file generated by the charmm-gui web made with XPLOR and I
have another psf file for the same system made with the autopsf gen from
VMD both made with the same topology file. The system contains a protein +
POPC + water + ions and there is a difference in the number of angles and
dihedral b/w both psf files. I found on the namd tutorial that the psf
files generated by xplor contain more or duplicated dihedrals. Could that
be the reason for my discrepancy?

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.