VMD-L Mailing List

From: Daniel Kennedy (kenne358_at_umn.edu)
Date: Mon Aug 20 2007 - 12:09:05 CDT

I am using psfgen to build a pdb file from a homology-modeled file I have
already built. I just select the entire protein, mutate a residue, and write
it to file. I am having a problem with one of my proteins, however. When I
use psfgen, I get a warning message saying that there is an unusual bond
between residue 204 (none) and other residues. Psfgen then fails to write
residue 204 to the pdb file. It seems that VMD thinks that residue 204 is
not a protein residue, but it is just a normal glutamine. I have never seen
this unusual bond message; why would I get it now?

Daniel Kennedy
Department of Physics and Astronomy
University of Minnesota