AMBER Archive (2004)

Subject: Re: AMBER: single amino acid energy

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Tue May 18 2004 - 10:23:26 CDT

> Helios Chen schrieb:
>
> Dear all, I wonder to calculate the single amino acid energy at the
> minimiz status in whole protein, how can I do? For example, a protein
> included 200 amino acid, and I want to calculate the minimized
> energy of 40th amino acid. Could anyone help me? Thanks in advance.

You might want to take a look at the mm_pbsa section, in particular the
decomposition part. You can feed mm_pbsa your restart file from the
minimization, provided you rename it as PREFIX_rec.crd.1 (where PREFIX
is specified in the mm_pbsa.in file).

Best regards

Holger 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++                             
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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