VMD-L Mailing List

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Fri Aug 20 2010 - 18:43:00 CDT

Dear VMD users:

I'm having some problems trying to convert the pdb and psf files of a
membrane protein with POPC generated using the CHARMM27 parameters to
the new CHARMM36 parameters. I have renamed the atoms in my pdb and tried to
use psfgen and/or autopsf to re-generate the psf with the new topology and I
get a estrange long bond between one oxygen atom and the P (P1) atom. Has
anyone been working with this? Can anyone help?

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