Rosetta remodel - including an RNA ligand

I have been trying to include an RNA as a ligand for some time now, and every attempt is a failiure. Can someone explain me how to put a whole ribonucleoprotein, RNA as ligand, into remodel? When i get a relaxed structure my interaction sites are messed up. So far i have been using constraints but i really need that RNA in there as a ligand for further research.