AMBER Archive (2002)

Subject: Re: MM-PBSA philosophy

From: Felipe Pineda (pineda_at_gawain.imb-jena.de)
Date: Wed Mar 20 2002 - 08:25:05 CST

dear Michal:

the following is an extract from the amber6 manual (p.318) on MM-PBSA:

"The mm_pbsa script can be used to calculate the energies for a single molecule
as well as a complex. In the latter case the mm_pbsa script uses the trajectory
of the complex and calculates the respective energies for the complex and all
interacting components by mapping the structures of the interacting molecules
from that one of their complex. Thus, the assumption is made that no
significant changes occur to the structures of the interacting molecules during
the complex forma- tion. However, when there is a such change to the
structures, then three separate sets of trajecto- ries should be collected for
the individual interacting components which should be sampled alone in
solution. These sets of trajectories should be processed individually with the
mm_pbsa script which will produce files with the extension *.all.out. These
files can be processed outside the mm_pbsa script with the program
mm_pbsa_statistics_independent to extract all energy terms and interaction
energies."

i hope it answers to your question.

Best regards

Felipe 

-- 
Dr. Luis Felipe Pineda De Castro
EnTec GmbH
Structural Bioinformatics and Drug Design
Adolf-Reichwein-Str. 20        Phone:  +49-3641-65-6493
D-07745 Jena,                  Fax:    +49-3641-65-8436
GERMANY 
e-Mail: pineda_at_imb-jena.de
web   : http://www.entec-jena.de