From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Mon Jul 25 2005 - 15:42:45 CDT

I'm postiing this to the VMD list since I use VMD during structure builds. In our system, we apply a variety of patches during the build process; in retrospect, it looks like this changes the canonical atom ordering in the patched residues--as an example, the carboxylate atoms from the CTER patch end up as the first atoms of the last residue. Unfortunately, CHARMM preserves canonical atom ordering during builds.

This becomes a problem when I want to analyze a NAMD-generated trajectory with CHARMM (in this case, stripping solvent and ions off prior to vibrational analysis). The bonding becomes garbled, since atom numbers have effectively been switched in the patched residues. Has anyone developed an easy way to either (1) convert the CHARMM PSF file to NAMD ordering, or (2) convert VMD/NAMD PSF file ordering to canonical?

Thanks,

Chris

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007