another symmetric docking question. What I want to do is symmetrically dock two ligands to a receptor dimer, the binding sides are between the two symmetric interfaces (its the tryptophan repressor dimer binding two tryptophans). When I try SymDock it docks the monomers, as its supposed to be, albeit not in the right way (the crystal structure). What I basically want is just symmetric ligand docking, it should leave the interface from the .sym file untouched, apart from minor adjustments if necessary. Maybe SymDock is the wrong approach in this context?
What does the "-symmetry:initialize_rigid_body_dofs" flag do? Is it a way to preserve the interface from the .sym file?