AMBER Archive (2004)

Subject: Re: AMBER: questions about NMODE

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 29 2004 - 14:03:54 CDT

On Thu, Apr 29, 2004, xhu1_at_memphis.edu wrote:
>
> 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
> *********************************************************************

Are you using the same dielectric model in the two calculations? If
everything else is the same except for the electrostatics, then it should
be possible for you to track down the origin of the differences.

...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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