AMBER Archive (2004)

Subject: Re: AMBER:

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Thu Apr 08 2004 - 09:20:51 CDT

> In the sander minimizer output there is a term "HBOND", and in the dynamics information there is a term "EHBOND". In all of my runs these are always zero. Can someone tell me what these terms mean and what would cause them to become nonzero?

>From an older reply:

"The HBOND term refers to a Lennard-Jones 10-12 potential, which has
been
used in the Weiner et al. force fields to describe non-bonded
interactions between hydrogen bond pairs. Starting with the Cornell et
al. force field (parm94), this term is omitted now, hence its value is
set to zero."

Best regards

Holger
 
>
> Thanks!
>
> John
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
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