Unfortunately, full global docking of protein/nucleic acid complexes isn’t yet possible in Rosetta (though people are working on it). The best you can currently do is the high-resolution refinement stage. That is, if you have the protein in approximately the right location (within a couple of Angstroms) you can repurpose the high resolution refinement stages of the protein-protein docking protocol to refine the protein/nucleic acid complex.
Although be advised that the energy functions used during the process have not been optimized for protein-nucleic acid interactions, so the results may not be as accurate as one might get if one were to have a protocol that was optimized for the use case.
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