AMBER Archive (2004)Subject: Re: AMBER: questions about NMODE
From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 28 2004 - 17:24:34 CDT
On Wed, Apr 28, 2004, xhu1_at_memphis.edu wrote:
>
> Normal mode analysis, coordinates have been minimized
> &data
> ntrun=1
> cut=8.5
^^^^^^
Your cutoff for nmode should be 9999., just as for sander. At the beginning
you should also set nvect (to a small number) as well.
...hope this helps...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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