Dear Amber users,
I have been using the MMPBSA.py script to calculate a drug-protein binding energy. For the Poisson-Boltzmann results, the nonpolar term is exactly zero for all the residue-wise decompositions. This is not the case for Generalized Born (although they are still all very close to zero).
Should I be surprised by this result and/or concerned that there is potentially a problem with the calculation? One rather unusual feature of my system is that the binding site is pretty much entirely enclosed at the interface of a protein-protein heterodimer (although water is still able to diffuse in and out of the site). I don't really know what I should expect based on this though.
Any input would be greatly appreciated.
Sincerely,
Andrew Kalenkiewicz
Postbaccalaureate Fellow, NICHD
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Received on Tue Feb 16 2016 - 12:00:03 PST
