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fff@bioinfo:~/Docking$ docking_protocol.linuxgccrelease @flags -database /usr/local/rosetta/3.1/rosetta_database
ERROR: Option matching -docking:dock_mcm not found in command line top-level context
This question has been answered before. The documentation is out of date. dock_mcm is the default mode and you don’t need a flag for it at all. (Why they didn’t fix this when we went from 3.1 to 3.2 is beyond me).