Re: [AMBER] MMPB(GB)SA: two questions

From: Cannon, John F. <>
Date: Mon, 5 Mar 2012 13:37:16 +0000

Dear George,

Question 1: Here are two references that might be useful to get started.

Hou T, Wang J, Li Y, Wang W. 2011 Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model. Jan 24;51(1):69-82.

Singh N, Warshel A. 2010 Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. Proteins. 78(7):1705-23.

Question 2: The clustering is probably based on interatomic distances and therefore configuration, not on energy. If you have 100-1000's of trajectory snapshots, why would you not want an average to make sure you did not choose an outlier?

John Cannon
Genetics Program Chair and
Associate Professor of
Molecular Microbiology and Immunology
University of Missouri
1 Hospital Drive
Columbia, Missouri 65212

-----Original Message-----
From: George Tzotzos []
Sent: Saturday, March 03, 2012 7:05 AM
To: AMBER Mailing List
Subject: [AMBER] MMPB(GB)SA: two questions

Hi everybody,

I'd like to ask if any can shed light on the following:

1. Is there any study comparing ÄGs obtained form MMPBSA and MMGBSA to experimental values?

2. Are ÄGs obtained from one or very few trajectory snapshot reliable? This because clustering analysis produces on occasions clusters with 1 or very few members.

Thanks in advance for any suggestions


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