AMBER Archive (2009)

Subject: [AMBER] GBSA: dielectric symmetry

From: Giacomo Bastianelli (gbastianelli_at_giacomobastianelli.com)
Date: Thu Mar 05 2009 - 17:29:50 CST

Dear Amber users,

I have been using MM_GBSA to calculate free energy of binding of protein
complexes and I have tried to optimize the internal and external
dielectric for maximizing the correlation with experimental data.
What I observed is that if I calculate the free energy with int-diel = 1
and ext-diel = 80 I obtain different results from the case of int-diel = 2
and ext-diel = 40. This is surprising since I was expecting the same value
because the symmetry in the GB formula: (1/int-diel - 1/ext-diel).
Am I missing something?

Thanks,

Giacomo

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