VMD-L Mailing List

From: brosbam_at_berkeley.edu
Date: Tue Jul 15 2008 - 12:37:30 CDT

This question is related to the VMD case study for light-harvesting in
purple bacteria. I am attempting to setup a NAMD simulation for the
acidophila-lh2.pdb structure included in the case study. To generate a
.psf I created aliases for atoms and residues as needed like in the
ubiquitin tutorial. However, I do not know how to treat certain residue
names that are not present in the topology file, namely "BCL" for the
bacteriochlorophylls, and "RG1" for the Carotenoids. Are there suitable
aliases for these residues as well? I suppose this is as much of a
bio-chem. question as a technical VMD one.
I plan to edit the files from a perl script by calling psfgen in vmd text
mode, btw.
Thanks.