AMBER Archive (2004)

Subject: Re: AMBER: questions about NMODE

From: xhu1_at_memphis.edu
Date: Thu Apr 29 2004 - 13:11:41 CDT

Dear Dr. Case,

Thank you for your suggestion. I tried both formated and nonformated
coordinate files. the error is same. I checked each piece of energy
from last step of sander and nmode output. looks like the energies
about electronic are different. The molecule is not neutrlized, and
has +1 charge. Maybe it is the reason???

Best

Xiaohua

nmode output:
********************************************************************
             E-ELE
         -0.23788E+04
             E-EEL14
          0.66102E+03
       E-POL E-3BOD
     0.00000E+00 0.00000E+00

******************************************************************

last step in sander:
**************************************************************

  EEL = -6260.3215
 1-4 EEL = 3637.1484
*********************************************************************

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Wednesday, April 28, 2004 7:21 pm
Subject: Re: AMBER: questions about NMODE

> On Wed, Apr 28, 2004, xhu1_at_memphis.edu wrote:
>
> > 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
>
> seems very large...are you using an unformatted coordinate file? You
> should examine each piece of the energy from the last step in
> sander and
> the nmode output to see if you can figure out what is going on.
>
> ...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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