Greetings Rosetta Team,
Now that I've resolved my ligand_docking issues (big thanks to Rocco!) I would like to generate and screen symmetric protein+ligand homo-multimer structures.
First, in order to get SymDock to recognize my ligand and generate output, I had to rename one of the ligand's carbon atoms "CA".
Not a big deal, but it required changing the name for each occurrence of the ligand (input .pdb, parameter files, and rotamer libraries).
For the test case, SymDock.linuxgccrelease was run using PBS on four cores with the following flags: