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 ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu