AMBER Archive (2007)

Subject: AMBER: MM-GBSA residues decomposition comparison

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Tue Mar 20 2007 - 08:17:26 CST

Dear AMBERs,

I'd like to ask you for advice how to proceed in the following
situation. I'm calculating MM-GBSA per residue energy decomposition for
SH3-domains within different complexes. As long as I wdealed with
SH3-domain complexes with peptides I obtained results easy to compare
with each other. Now I face some difficulties when I try to compare the
results obtained for the single molecule, containing SH3-domain (in that
case I had to consider the whole molecule as the receptor and then
decompose the energy) and complexes of SH3-domian and other proteins as
separate molecules (in this case I consider SH3-domain as receptor, the
rest as the ligand). As I understand it is quite natural that I cannot
compare the energies obtained in these different cases for corresponding
residues even if they are participating in similar interactions. Then
the question is: do you think that if I recalculate energy decomposition
for the separate molecules considereing them all together as 'one
receptor' I could get the values I could then use to compare with the
results obtained for real 'one molecule' case? Or (I think it's rather
like this) the difference of the system would not allow to compare these
values anyway?

Thank you very much in advance!

Sergey
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