RE: AMBER: why not minimize snapshots before MM/PBSA calculations

From: Arnoult, Eric [PRDFR] <>
Date: Wed, 27 Jul 2005 09:21:30 +0200

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




-----Original Message-----

From: []On Behalf

Of JunJun Liu

Sent: Tuesday, July 26, 2005 5:02 PM


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!


JunJun Liu
College of Chemistry
Central China Normal University
WuHan 430079
P.R. China
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 27 2005 - 08:53:00 PDT
Custom Search