On Wed, Sep 10, 2014 at 2:54 PM, Ahmed Ayoub <atayoub.ualberta.ca> wrote:
> 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?
>
​Decomposition calculations use a different surface area algorithm to
compute the SASA used in computing the nonpolar solvation free energy. So
if you are comparing against a run that does _not_ specify a &decomp
section to the input file, this is the likely culprit.
HTH,
Jason
​
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 10 2014 - 12:30:03 PDT
