AMBER Archive (2001)

Subject: free energy contribution of selected atoms vs. MM-PB/GBSA

From: Michal Otyepka (otyepka_at_aix.upol.cz)
Date: Fri Aug 17 2001 - 06:25:55 CDT

Dear AMBERs,

I wanted to evaluate contributions of selected atoms to interaction energy
between inhibitor and protein. I run 1ns MD and then analyzed trajectory
using by MM-GBSA method. Then I pertrubeb partial charge (in all
neccessary files) of one atom from aprox. -0.300 to 0.000e and run MM-GBSA
script again. The result was surprising because of high difference in the
total energy (aprox. 100 kcal/mol from -7 to 90 kcal/mol, the highest
change occured in electrostatic energy).

I have two questions? Could be MM-PB/GBSA method used for evaluation of
delta G selected atoms (free energy contribution of selected atoms)? Why
was the delta G so big?

Does anybody have any suggestion?

With best regards, Michal Otyepka

P.S. Really, I know FEB method but it is very time/source consuming
method.

      
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