From: Chris Harrison (
Date: Sun Feb 05 2012 - 15:45:19 CST

No. You'll need a topology file. Why not create the topology file?
CHARMM is an additive forcefield.


On Sun, Feb 5, 2012 at 2:13 PM, Rajan Vatassery <> wrote:
> Hi All,
>        I am looking for a way to avoid creating a topology file whenever I
> need to create a new PSF. For example, my current need is for a PSF for
> oleic acid. I can easily create a pdb file, but the creation of a PSF is
> substantially more time-intensive. Currently I would need to make a
> topology file, which although is not terribly difficult, is not used
> after the creation of the PSF.
>        My hope is that there is some way that I can use the bonds given in the
> pdb file to produce the essential details that PSFGEN needs to then go
> on to writing the angles and dihedrals. As it is now, if I try to create
> anything in terms of a segment for writing (segment U {pdb Oleate.pdb}),
> I get the usual:
> unknown residue type
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.
> because I haven't given a topology file to PSFGEN.
>        My impression is that during the normal PSF creation from a topology
> file, PSFGEN calculates the angles and dihedrals from only the list of
> bonds that are given in the topology file. So my question stated in
> another way is, can I trick PSFGEN into reading the bond list from the
> PDB file? I would even rather write the first part of the PSF (atoms and
> bonds) if I could get the angles and dihedrals automatically generated.
> Thanks in advance,
> rajan

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 773-570-6078                Fax: 217-244-6078