AMBER Archive (2009)

Subject: [AMBER] MM-PBSA results

From: Dmitry Osolodkin (
Date: Fri Aug 07 2009 - 09:31:48 CDT

Dear List,

During MM-PBSA analysis of a series of similar trajectories (same
protein, same ligand but different positions of the ligand on the
surface of the receptor) I get dissimilar results. Namely, for three
trajectories the values for PBTOT and GBTOT are similar, but for
trajectory IV they are very different (see table). This difference is
due to very unsimilar values of PBCAL and GB.

I -40.08 -25.61 -26.39 -23.49 -2.12
II -29.69 -17.19 -17.88 -24.75 7.56
III -40.37 -17.49 -18.55 -19.55 2.06
IV -42.93 -14.35 -28.13 -16.40 2.05

The outlying GAS value for trajectory II is just due to fluctuations and
the error of subtraction. So, there are two questions:

1. What is the reason for the difference between PBTOT and GBTOT?

2. Which one should be used for deltaG estimate? It is obvious that
usage of GBTOT instead of PBTOT gives opposite results.

Thanks in advance.
Dmitry Osolodkin.

Dmitry Osolodkin
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
Phone: +7-495-9393557
Fax: +7-495-9390290

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