From: flavio seixas (
Date: Sun Feb 05 2012 - 18:24:40 CST


You may try swiss param (
The output file generated contains: *.pdb, *.psf, topology and parameters files in Gromacs or Charmm formats.

Of course, if you need accurate force fields you must to improve topology (bonds, distances and charges) using Gausian Software.



--- On Sun, 2/5/12, Rajan Vatassery <> wrote:

> From: Rajan Vatassery <>
> Subject: vmd-l: PSFGEN and Reading Bonds from PDB Files
> To:
> Date: Sunday, February 5, 2012, 8:13 PM
> 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
> 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