VMD-L Mailing List

From: Rajan Vatassery (rajan_at_umn.edu)
Date: Sun Feb 05 2012 - 14:13:43 CST

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