AMBER Archive (2002)

Subject: Re: Amber7 and VMD

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Wed Apr 10 2002 - 08:55:46 CDT

> I am not able to see the amber results(Amber7) using VMD anymore.
> I had no problem with amber6 previously. (VMD-1.7.1)
> Inside VMD, I use "parm and crd" to view movie generated with Amber.
>
> I noticed that amber "parmtop" file format has been changed in amber7

In the meantime, before a general purpose prmtop converter is available
and before the various other accessory programs update to the new
AMBER-style prmtop format are available, you can use a feature in rdparm
to write out an older style parmtop... This is with the command
writeparm.

$AMBERHOME/exe/rdparm prmtop.new
writeparm prmtop.old
quit

[This will work as long as the new prmtop doesn't contain additional
information beyond what was previously in the old prmtop format--any new
information will be lost--but the prmtop should still be good for viewing
movies. As yet there is no old to new prmtop converter except for
rebuilding with LEaP.]

I have successfully used this for watching VMD movies.

Thomas E. Cheatham, III
Department of Medicinal Chemistry & Center for High Performance Computing
University of Utah INSCC 418 & BRPB 295A
30 South 2000 East, Room 201 155 South 1452 East
Salt Lake City, Utah 84112-5820 Salt Lake City, Utah 84112-0190
tec3_at_utah.edu http://www.chpc.utah.edu/~cheatham
phone: (801) 587-9652 FAX: (801) 585-5366