Hello Liu,
You can read this paper :
Validation and Use of the MM-PBSA Approach for Drug Discovery
Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M.;
J. Med. Chem.; (Article); 2005; 48(12); 4040-4048. DOI: 10.1021/jm049081q
The Authors minimized the snapshots before MM/PBSA calculations.
Kind Regards
éric
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu]On Behalf
Of JunJun Liu
Sent: Tuesday, July 26, 2005 5:02 PM
To: amber.scripps.edu
Subject: AMBER: why not minimize snapshots before MM/PBSA calculations
Dear AMBER Users:
If there's only one snapshot when performing MM/PBSA calculation for the
binding free energy, I think it's necessary to minimize the structure to
local minimum to obtain the lowest energy. However, when there's a MD
trajectory for one to evaluate the binding free energy, no
energy-minimization will be performed for MM,GB, and PB calculations. My
question is, why not minimize the snapshots until convergence before
MM,GB,PB,NM calculations? Thanks in advance!
Best Regards!
Liu
--
JunJun Liu
College of Chemistry
Central China Normal University
WuHan 430079
P.R. China
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Received on Wed Jul 27 2005 - 08:53:00 PDT
