---------- Forwarded message ----------
From: manikanthan bhavaraju <manikanthanbhavaraju.gmail.com>
Date: Wed, Mar 7, 2012 at 4:23 PM
Subject: Comparison of the results
To: AMBER Mailing List <amber.ambermd.org>
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
comparison.
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?
Thanks,
mani
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Wed Mar 07 2012 - 23:00:03 PST
