VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Feb 05 2012 - 15:36:29 CST

On Sun, Feb 5, 2012 at 3:13 PM, Rajan Vatassery <rajan_at_umn.edu> 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.

perhaps the approach in the topotools plugin is more suited to your needs.

http://sites.google.com/site/akohlmey/software/topotools

>        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

please note, that psfgen takes not only bonds and angles
from the topology file, but also assigns atom types and
(partial) charges, not to mention that it can recreate missing
atoms (e.g. hydrogens)

> 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

no. but if there *are* bonds in the pdb file (there usually are none),
the pdb reader plugin will use them. usually VMD guesses the
bonds based on a simple distance criterion and what it guesses
as elements for the atoms. you can just write out a psf file based
on that information from the pdb file. it will, however, not be suitable
for simulations, unless you augment the internal information in
VMD with the missing pieces, e.g. from tcl script code.

this is where topotools steps in, as it provides abstractions
for more complex operations, that would otherwise require
significant experience in Tcl/VMD scripting.

in any case, neither tool can generate information from nothing.
psfgen is database (= topology file entry) oriented and thus fairly
rigid in how things need to be done and topotools gives you more
freedom, but requires you to be more careful as to what you do.

axel.

> bonds) if I could get the angles and dihedrals automatically generated.
>
> Thanks in advance,
>
> rajan
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.