AMBER: why not minimize snapshots before MM/PBSA calculations

From: JunJun Liu <>
Date: Tue, 26 Jul 2005 23:02:00 +0800

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
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Received on Tue Jul 26 2005 - 16:53:03 PDT
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