AMBER Archive (2004)

Subject: Re: AMBER: how to use mm_pbsa_statistics.pl independently

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Tue Apr 13 2004 - 12:06:43 CDT

> Jufang Shan schrieb:
>
> Hi,
>
> I want to calculate the binding free energy between receptor and
> ligand. I calculated the entropy for the complex, receptor and ligand
> using normal mode separately since the same parameters don't work for
> all. My question is what value shall I give to "calc delta" (?0..1)
> and "calc decomp" (?0..2) to run mm_pbsa_statistics.pl? I am using
> Amber 7.

If the snapshots of com, rec, lig are from three different trajectories,
use calc_delta = 2. If the snapshots were extracted from the same
trajectory, use calc_delta = 1. For both cases, set calc_decomp to 0.

Best regards

Holger

>
> Thanks,
> Jufang
>
> ----------------------------------------------------------------
> Jufang Shan
> Graduate Student
> Dept. of Structural Biology
> St. Jude Children's Research Hospital
> Interdisciplinary Program
> The University of Tenessee Health Science Center 

-- 
!!!      Please note new telephone number      !!!
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik

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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