Visualizing AMBER coordinates trajectory in VMD

From: Pratul Agarwal <>
Date: Mon 4 Nov 2002 12:54:57 -0800 (PST)


Is it possible to use VMD to visualize an AMBER trajectory (generated by
sander), which has only solute coordinates saved? My system has explicit
solvent but to save disk space I only saved the solute coordinates. When
I load the parm and crd file in VMD, the display looks strange, my guess is
that this is because of missing solvent coordinates. Is there any way to fix

Also is anybody aware of any PC/Linux based tool which can be used to
animate normal modes (generated by nmode and quasih)?


Some info:

AMBER v7.0, parm file converted using new2oldparm
both crd and crdbox option used in VMD.

VMD version 1.8a21

Do you Yahoo!?
HotJobs - Search new jobs daily now
Received on Mon Nov 04 2002 - 12:54:57 PST
Custom Search