[AMBER] Comparison of the results

From: manikanthan bhavaraju <manikanthanbhavaraju.gmail.com>
Date: Wed, 7 Mar 2012 16:23:54 -0600

Hi All,
I have performed thermodynamic integration using amber8 anf ff99, I
have calculataed deltaA for protein-ligand system. Later with
Ambertools 1.5 (mmpbsa.py) MM-PBSA, MM_GBSA, and NAB were done. When
the TI results are compared with GBSA/PBSA +NAB, I am getting
conflciting results.

TI results deltaA = -9.2 kcal/mol

MM-PBSA = -19.27 +/- 3.09 kcal/mol
MM-GBSA = -11.85 +/-2.34 kcal/mol

NAB (entropy) = -19.59 +/- 4.16 kcal/mol (10 snapshots)

The PBSA and NAB values are nearly equal. But when I take the
difference between GBSA and NAB values, the deltaG= +7.74 kcal/mol.
There are no experimental values avaliable for my system for

I have done some literature search on free energy of binding. In some
of the papers, the GBSA/PBSA were lower than NAB/nmode values. Are my
NAB values meaningful?

Any suggestions?


Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
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Received on Wed Mar 07 2012 - 14:30:03 PST
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