I have some known protein complex(two chains) and would like to calculate the binding energy of each complex. I don't want to dock any more but just score the binding energy. I have done a fast relax for chain A and chain B, and then combine them into the same pdb file, then use docking prepack to generate the input structure. (should I avoid the fast relax for individual chain but direct use dock prepack to generate the input structure?)
But I don't know which option to calculate the binding energy. Thanks for help.
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protein binding energy problem