How do I identify two ligand residue type files? I'm docking two proteins, each with a prosthetic group that's near the docking interface. I've created the residue type files. I can only get it to recognize one of the two residues, whether I use -extra_res_fa [They're both in the same dir], or whether I use two -extra_res_fa statements, or if I string the full path & file names of both files after the -extra_res_fa statement. A while back, someone explained to me that I can also put the .params files into rosetta_database/chemical/residue_type_sets/fa_standard/residue_types & add the appropriate lines to the file residue_types.txt. Well, I tried that. No go. When I went back to the -extra_res_fa flag, I got an error message that 'residue type names must be unique' or something close to it. So it's sort of recognizing I put something in there, even if it refuses to use it. I renamed the edited residue_types.txt file & moved the original back in place, but I'm still stuck.
Yes, I should probably upgrade to 3.2, but I REALLY need this to run. After that, I can think about it.