[AMBER] selecting the best docking pose with MM/PBSA

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Tue, 9 Dec 2014 01:22:39 +0200

Dear AMBER list,

I have 3 posing docking poses of a compound. Does calculating relative free
energies of binding with MM/PBSA (without the normal mode approximation)
help selecting the predominant one? I know MM/PBSA makes a lot of very
large assumptions and the differences in the final relative free energies
may be within the error of the method. There is also a dependence on the
ligand force field which determines how strained a conformation is in the
protein. I am just curious to know if other people use this methods to
select the best among a few docking poses.

thanks in advance,
Thomas

-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
          tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===============================================================
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
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Received on Mon Dec 08 2014 - 15:30:02 PST