Dear Sir/Madam,
I did a protein-drug complex MD study. I calculated the MM/GBSA per-residue analysis. I found the drug has a per-residue energy too, what is the physical meaning of this number? Should we interpret it as the internal binding energy of the drug at gain or loss upon binding with the protein? My gut feeling is when we are talking about per-residue energy, I should only got the energy for protein residues, I am not quite sure why the drug have energy contribution to it too. Please kindly instruct.
I also did a MM/GBSA total binding energy for the same complex, why it is different from the sum of MM/GBSA per-residues' total energy?
Best regards,
Annie
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Received on Sun Feb 26 2012 - 23:30:03 PST
