I've been having some issues in modifying my dock.xml file for a multiple ligand docking run. I been trying to use the paper "RosettaLigand docking with flexible XML protocols" as a reference but no luck. According to the paper I should be trying to modify the <LIGAND_AREA> and <INTERFACE_BUILDER> taggs, but the paper only shows an xml file for a single ligand dock. I'm pretty new to this and rosetta scripts, so I'm not sure exactly how to proceed. Anyhelp would be appreciated.
On a side note, how should my starting receptor-ligand pdb file be formated (I am trying to dock an identical ligand to each monomer of a homodimer complex). So far I have concatonated the ligand.pdb info to the end of my clean dimer PDB and then changed the residue count. Not sure if I should keep both ligands as "X" or make one "Y" to distinguish between the two.
I will post both files as refernce