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in case you haven’t found a satisfying solution, i’d suggest using an enzdes style constraint file to specify the cofactor as covalently bound. check out the enzdes cstfile documentation at http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_match_enzdes_cstfile.html
i’d make a cstfile containing one block, which specifies a constraint between the two atoms that are covalently bound. the force constants can be set to 0, but the constraint block needs to be declared as covalent.
once you have the constraint file, simply reference it one the command line with -enzdes:cstfile