Re: Visualizing AMBER coordinates trajectory in VMD

From: David A. Case <>
Date: Mon 4 Nov 2002 13:57:10 -0800

On Mon, Nov 04, 2002, Pratul Agarwal wrote:
> 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
> this?

You should be able to construct a modified prmtop file in one of two ways:

(a) go back to your LEaP script, and re-run, omitting any "solvate" and
"addIons" commands.

(b) use rdparm, with the commands "stripwater" and "writeparm".

Then you should have a prmtop file that has not waters, and hence is "in sync"
with the trajectory file.

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Mon Nov 04 2002 - 13:57:10 PST
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