Dear Amber users,
I want to calculate the binding free energy of a water molecule which forms stable hydrogen bonds with the protein in the protein-ligand binding pocket. Can I simply treat this water molecule as a ligand, and calculate the protein-water binding free energy with MMPBSA method ? I am looking forward to your reply, thanks in advance !
Yours,Jinfeng Liu.
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Received on Wed Jul 04 2012 - 22:30:02 PDT
