VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Aug 20 2007 - 16:48:00 CDT

Hi Daniel,

Daniel Kennedy wrote:
> 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.
The unusual bond warning is probably immaterial here, as it is just
reporting its findings from a distance based search, and psfgen will
ignore this. You might be getting it now if your mutation lead to a
situation where two atoms are closer to each other than would normally
be expected (which can happen fairly easily, if you just dropped in one
side chain to replace another).
> 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?
>
It would be helpful if you could elaborate on exactly how you're trying
to generate the file, ideally with a snippet of your pdb file (say the
glutamine and the last 2-3 residues before it) and your psfgen script.

Best,
Peter