[AMBER] Total vs per-residue MMGBSA energies

From: Ahmed Ayoub <atayoub.ualberta.ca>
Date: Wed, 10 Sep 2014 12:54:20 -0600

Dear Amber users,

I have a protein receptor of 1738 residues, and a small ligand. I then
calculate total and per-residue MMGBSA binding energy. However, in MMGBSA,
I requested amber to print the decomposed energies for all the residues in
the complex (namely the 1739 residues).
Then I compared the total binding energy to the sum of all the individual
per-residue energies of all the 1739 residues. It turns out that the two
values are slightly different (-36.24 vs -37.42 kcal/mol, respectively). I
tried this with different cases and different systems and the two values
are always slightly different. Could any one explain that?
Any help is appreciated.

Ahmed Taha Ayoub
PhD Candidate, Theoretical and Computational Chemistry
W4-54, Department of Chemistry
11227 Saskatchewan Drive
University of Alberta
Edmonton, Alberta T6G 2G2
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Received on Wed Sep 10 2014 - 12:00:02 PDT
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