VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 27 2007 - 12:04:09 CDT

As an addendum to that... I'm not an amber user (program or forcefield),
so if anyone does have the files that Bob is looking for, please send
them to me as well and I'll see that they're included in future releases.
Thanks,
Peter

Bob Johnson wrote:
> Hello everyone,
> Ulitmately, I am trying to use the NAMD Energy plugin in VMD 1.8.6. However, I
> think most of my problems stem from not having a PSF file for my system. All my
> work is done using the Amber force field ports in Gromacs. Thus, to use NAMD
> Energy, I'm trying to convert my system into a PSF file (I assume there is no
> way
> around this) with the Auto PSF plugin.
>
> I noticed that there are Amber topology and parameter files in the
> readcharmmtop1.0 and readcharmmpar1.0 directories. However, they do not contain
> topologies for DNA or terminal DNA residues. Does anyone have these files or are
> patches available?
> Thanks,
> Bob
>