[AMBER] Fwd: Comparison of the results

From: manikanthan bhavaraju <mhb75.msstate.edu>
Date: Thu, 8 Mar 2012 00:31:48 -0600

---------- 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

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 - 23:00:03 PST
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