Something has eaten my original response – the first posting from “smlewis” above is not from me, this appears to be a response from mahajanr.
The response to the original question, which got overwritten: Yes, you have to make N directories to run on N processors. The docking executeable in Rosetta3 predates the more recent job distributor, and the maintainers have not ported it to the unified job distributor/MPI system.
I am not aware of a filtering option in the main docking executeable. I believe you can get filtering using the parser version instead (I believe the documentation calls it “dock-design” or something similar).