AMBER Archive (2004)

Subject: Re: AMBER: questions about NMODE

From: xhu1_at_memphis.edu
Date: Wed Apr 28 2004 - 18:04:04 CDT

Thanks again, Dr. Case! But I still got the same error message:
 
 Root-mean-square gradient of input coords is 2.10789907
 This is greater than the requested maximum: 1.E-05

Regards

Xiaohua

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Wednesday, April 28, 2004 5:24 pm
Subject: Re: AMBER: questions about NMODE

> 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
> beginningyou 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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