AMBER Archive (2009)

Subject: [AMBER] About Free energy decomposition

From: Rajesh Raju (Rajesh.Raju_at_postgrad.manchester.ac.uk)
Date: Wed Mar 25 2009 - 09:08:00 CDT

Hi,

I have a doubt about MM-GBSA free energy decompostion with ligand and
some residues. I found in literacture that the one half of the
pairwise VDw interacation energy divides equally between the
interaction pair... That means
  if the total interaction energy is 10 kcal mol-1 for the interaction
between Res A -Res B, the MM-GBSA output will show 5 kcal mol-1 for
Res A and 5 kcal mol-1 for Res B Is that true? I think electrostatic
energy also divide equally between Res A and Res B. When I did QM
interaction energy for one residue and ligand i got an interaction
energy almost double.

I have doubt about the solvation parts. The free energy decomposition
results show GB and SASA energy term for residues. Are these values
also divided between them

Many thanks
Rajesh

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