Dear Aneesh
in my opinion using MM is not the best choice to extimate the p-p
interaction, i would use something Quantum.
In Amber there are some semiempirical methods, maybe you can use one of
these, but preliminary you need to evaluate the best methods for p-p
interaction.
To extimate the p-p interactions maybe you can do something like alanine
scanning, you can do this using MM (or also QM, in this case you can use
simple models of the binding site).
Good luck
Jacopo
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Received on Fri Apr 03 2009 - 01:08:20 PDT
