I have a complex of one monomer binding a peptide. I would like to optimize binding energy instead of the default total energy by designing the protein binding site using the fixed backbone design protocol. I'm aware that it is probably not as simple as changing the score option flag, since binding energy score is total energy of the complex minus the sum of total energies of the docking partners. If this is correct, I'm wondering how to modify the protocol code. I guess that setting the scorefunction as something like core::scoring::ScoreFunctionFactory::create_score_function("docking") will not work, right? Do I need to explicitly define the binding energy in the protocol code? Could you provide some code as an example?
Thanks a lot!