I have been having a world of trouble getting this exact scenario to work as well. Required is a .fasta file with the run name (t000.fasta) and fragment libraries (which I generated from Robetta and renamed aat000A03_05.200_v1_3 and aat000A09_05.200_v1_3). I also have a pose_loops file called t000.pose_loops containing a single line with my start and end residue defining the loop that I would like modeled. And finally there is a t000.pdb file that contains protein 1 (chain A) and protein 2 (chain B) separated by a TER statement.
When I run the following with the above files, I see the subsequent error:
rosetta aa t000 A -s t000.pdb -dock -pose -loop -randomize 1 -nstruct 1
"Number of residues in pdb file 420 disagrees with total_residue: 314"
So I inferred that my .pdb file containing both proteins should contain only one protein. Sure enough, when I remove the second protein and run the same command, I get:
"Docking partners are goofy....this simulation's hosed. Did you forget a TER statement?
Any help is weclomed