AMBER Archive (2009)

Subject: Fwd: [AMBER] MM-GBSA Free enegy decomposition

From: Rajesh Raju (Rajesh.Raju_at_postgrad.manchester.ac.uk)
Date: Tue Apr 28 2009 - 06:28:17 CDT

Hi,
I Performed free energy decomposition on per residue basis with my
ligand and protein. The output shows values almost half of which i got
from QM calculations. I read from some previous papers that

' one half of the pairwise electrostatic (vander waals) energy between
2 atoms each belonging to a different monomer is attributed to both of
them'

So that means the printed output for the gas phase energy (ELe+VDW)
ResA with ligand will be half the value given by QM energies . Am I
correct?

Also if thats the case printed solvation energy terms also half the
actual value?

Could anyone clarify my doubts..Its confusing me

Thanking you in advance
Rajesh

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