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: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Mon Nov 04 2002 - 13:57:10 PST
