Reply To: Can Rosetta generate proteins with sidechains ?

Most Rosetta modes output the sidechains. I assume you’re using abinitio mode without some of the fullatom flags. The abinitio documentation might tell you how to do it. If abinitio doesn’t say, then the fixbb executeable will happily add sidechains for you.

I would suggest flags something like this:
-packing:repack_only
-ex1 -ex2 -ex3 -ex4
-extrachi_cutoff 0
-minimize_sidechains
-run:min_type dfpmin_armijo