Dear Community;
It is well scripted that binding free leads to funny results which varied
publication wise for same complexes in different cases. Also the positive a
negative contribution in MMPBSA is not well scripted in any Amber manual. I
believe that Macromodule Embrace calculation from Schrodinger leads to a
better binding free compared with ITC than Amber MMPBSA/MMGBSA
scripts.Thats a different part and I think work is going on to generate a
better binding free profile descriptors.
I have some crucial question:
What a positive and negative value signifies in the contribution of E vdw;
E elec, G sol, Ggas ? Will be highly grateful if the community please
explain what a positive and negative decomposition on these descriptors
stands for and its correlation with Gbind and probable explanation in
protein-liagnd binding favourability?
Cheers!!
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Thu Feb 13 2014 - 22:30:02 PST
