From: Rose, Stuart Wallace (
Date: Tue Aug 05 2014 - 19:30:02 CDT

I ran CHARMM gui and I am now trying to add co-factors, since my 'collaborators' did not format co-factor topologies to patch in co-factors I have had to rename residues in CHARMM gui output. Accordingly, I have broken the output into segments and now I am reassembling with psfgen. The membrane lipids TOCL2 were renamed to TOCL (the psf residue type does not travel with the pdb) during writing the pdb for the MEMB segment.

How do I generate a complete system with psfgen with a membrane segment having cardiolipins named TOCL2? Is there a way to use the mutate command?

All the answers I think of require modifying topology RESI names or otherwise messing up the system to accommodate VMD which seems excessively complicated and not reproducible.

Thank you,

Stuart W. Rose
University of Illinois @ Urbana-Champaign

Center for Biophysics & Quantative Biology