On Tue, Jan 07, 2003, Jian Zhang wrote:
>
> In the output file of Sander, does the Etot include
> the energy of waters (I add some thousands of waters
> around the protein)? If so, how can I get the totaly
> energy of protein only, must I write programs to
> analysis the topology and trajectory files of sander
> myself?
See the mm/pbsa section of the manual.
> And What's the unit of velocity in mdvel file?
See the FAQ on "units" at the Amber web site.
>
> some FAQ questions, sorry.
We *do* encourage people to look at the FAQ before posting questions here.
..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
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Received on Wed Jan 08 2003 - 08:09:43 PST
