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
Canada
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 10 2014 - 12:00:02 PDT
