AMBER Archive (2008)

Subject: AMBER: energy decomposition vs ala scan

From: Sergio Wong (swong_at_mccammon.ucsd.edu)
Date: Mon Apr 14 2008 - 21:05:41 CDT

Dear Amber users;

    I'm performing a MMPGBSA study on a protein-protein
complex. The problem is that results from a compuational ala scan
calculation are significantly different than the corresponding data from
an energy contribution decomposition (per residue) calculation. While
these are not exactly the same quantities, I'm surprised they are so
different ( ~ 3 vs 40 kcal/mol). I'm wondering if anyone could clarify
exactly how the energy decomposition is computed. The same trajectory was
used for both calculations, so there is no "perturbation" due to the ala
mutation. Therefore, I'd expect a difference on the order of 1/2 rather
than 1/10. It might be worth mentioning the largest differences are for
Glu residues.

The options for the decomposition calculation are:

DCTYPE 2
#
COMREC 84-214
COMLIG 1-83
COMPRI 1-214
RECRES 1-131
RECPRI 1-131
RECMAP 84-214
LIGRES 1-83
LIGPRI 1-83
LIGMAP 1-83

Thanks;

-Sergio
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