VMD-L Mailing List

From: Bob Johnson (robertjo_at_physics.upenn.edu)
Date: Wed Jun 27 2007 - 11:55:44 CDT

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