AMBER: mm_pbsa

From: Wei Chen <>
Date: Wed, 9 Nov 2005 14:51:01 -0500

Hello, all Amber users,

I am using mm_pbsa in Amber8 to calculate binding free energy of two-protein
binding. When I used PB or GB to calculate polar solvation energy, I got very
different values. The free energies (not including entropy) are 93.28+/-90.46
kcal/mol with PB and -37.43+/-5.54 kcal/mol with GB. First of all, the mean
value with PB is positive, which doesn't make any sense. And the standard
deviation with PB is so large that it is the same order as the mean value. The
value with GB seems to be more acceptable. However, I think that GB is an
approximation to PB. So anybody can help me to understand the results?


Wei Chen

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Received on Wed Nov 09 2005 - 20:53:01 PST
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