I assume you use Rosetta 3.4, from our correspondence. Next release will include multichain receptor support. Meanwhile, what you are doing is OK and should work. If you are having a trouble with it, please post a log file of the run and the pdb.
If I use the different chain name for each chains of receptor, what will happen? I mean, what is the different between set same chain names and different chain names of receptor?
can you explain more to me?