I'm using version 3.1. I'm a bit confused about if snugdock and antibody modelling can be done in 3.1. both mention the command rosetta.gcc which I don't seem to have.
-is snugdock an option in the docking_protocol.linuxgccrelease? Or is snugdock to be downloaded separately and installed to be used with 3.1?
-what command is used for antibody modelling in 3.1?
-after generating say 10000 structures, how can I sort the results based on the rms and total score (here I'd be comparing with the native complex, so I assume I can take the decoy with the least rms).
many thanks in advance.
p.s. Thanks again to smlewis for posting the answer again to an earlier question.