From: Axel Kohlmeyer (
Date: Thu Jul 16 2009 - 17:30:59 CDT

On Thu, 2009-07-16 at 17:06 -0400, wrote:
> Hello,

hello adrienne,

> I am trying to create a psf file based on a pdb file of a molecule
> that is not a protein and would technically not have a classification
> in a topology file. When the pdb file was created the residue name was
> called MOL because there was not anything else it could have been
> called. The molecule is made up of carbon rings with hydrogen and a
> ammonia tail. Now since the residue name is not in a topology file it
> is not being recognized by psfgen so I keep getting the error:


> building segment M
> reading residues from pdb file rider-molecule1
> unknown residue type
> extracted 1 residues from pdb file
> Info: generating structure...
> unknown residue type
> ERROR: failed on end of segment
> MOLECULE MISSING! Use resetpsf to start over.
> MOLECULE MISSING! Use resetpsf to start over.
> MOLECULE MISSING! Use resetpsf to start over.
> MOLECULE MISSING! Use resetpsf to start over.
> Is there anything I could put in the residue column that would allow
> me to generate a psf or is there anyway for me to tell psfgen to
> ignore the unknown residue? Thank you.

psfgen will ignore the residue, if it is not there.
so you could load the original .pdb file and then type
in the vmd console:

set sel [atomselect top "resname not MOL"]
$sel writepdb part.pdb

and then try using psfgen for the part.pdb file.

of course that does not generate anything in the .psf
file for the non-standard residue. if you need that,
things can become a little bit more difficult.


> Sincerely,
> Adrienne LaFleur
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.