From: Axel Kohlmeyer (
Date: Fri Jul 04 2014 - 10:47:12 CDT

On Jul 4, 2014 7:42 AM, "Christian Wohlschlager" <> wrote:
> Dear Vmd' ler !
> I have a betaQA as a Cluster ( ~ 1800 Atoms) i try to make a psf file
for it to make i namd geometry calc. but i didnt found out how to correctly
make ( with autopsf) a .psf file. I think ????? the problem is that this
structure isnt a protein.
> can anybody give me a hint.

autopsf uses psfgen as the backend. It is meant to simplify routine cases,
for any non-standard you may be better off using psfgen directly.

For that you have to understand how this works. It reads a pdb file and
matches each contained residue against the topology file. If a match is
found, atoms are assigned types and charges, bonds defined, missing atoms
added and impropers added and so on. So first you need to make sure you
have that and that your file conforms to the expected conventions.

If you want even more control or need to make modifications, you can script
it with the topotools plugin.

> mfg
> christian
> -- Johannes Kepler Universitaet
> -- Christian Wohlschlager
> -- Altenbergerstr.69
> -- 4040 Linz Austria
> -- Tel: +43 732 2468 8595
> -