I'm dealing with a homodimer, in which the ligand is adjacent to the interface between the two monomeric subunits. I want to conduct an MD simulation to (a) find out atomic interactions; (b) find out the binding energy of the ligand (this is to be compared to the one I obtained by running simulations on the monomer).
My question is the following. In preparing the ligand, protein and complex topology files, is it legitimate to consider the two monomeric subunits PLUS one of the ligands as the PROTEIN? Alternatively, could I construct the complex by renaming one of the ligands and appending both ligands to the protein (homodimer)?
I'd be grateful for any suggestion.
Best regards
George
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Received on Fri Nov 29 2013 - 11:00:02 PST
