this is a little confusing to me, but if you have a binary protein complex, you can separate them into two files, one for each protein, do a sequence-alignment and then thread your sequence (change the template protein’s sequence to your target sequence) on to your respective template proteins using the partial_thread app in rosetta.
following the tutorials at http://www.meilerlab.org/index.php/rosetta-tutorials will probably help you there.
Once you have threading done, you could then combine the structures back together in something like pymol or just a text editor, and use RosettaCM in order to refine the models, giving it both your target sequences as a fasta file with a forwardslash separating the two (it must be in the same order as your pdb file)
Not sure if that makes sense, but that’s how I would do it!
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