AMBER: entropic energy

From: Nina Fischer <>
Date: Fri, 24 Feb 2006 13:15:17 +0100 (MET)

Dear all,

I am trying to calculate the relative binding free energy between
protein-DNA complexes with the GB model.
The binding energy contributions I calculated so far are
(enthalpic term =): G(polar), G(non-polar), and E(MM).

Do I need to calculate the entropic term (with translational, rotational
and vibrational contributions) as well or can I leave it out?
If it is possible to leave the entropy out while calculating the relative
binding free energy because it is constant does anyone know good
Otherwise what is the easiest way to calculate or estimate the
translational, rotaional and vibrational contributions?

thanks a lot!


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Received on Sun Feb 26 2006 - 06:10:18 PST
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