AMBER Archive (2005)

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

From: Arnoult, Eric [PRDFR] (EArnoult_at_prdfr.JNJ.com)
Date: Wed Jul 27 2005 - 02:21:30 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu]On Behalf

Of JunJun Liu

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

To: amber_at_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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