Here’s a reply from Ben Stranges:
“I guess the documentation isn’t very clear on this. They are using the wrong PDB as input for the docking step, everything up until that point looks good.
After you run the make_symmdef_file.pl script there are several outputs. The one that the symmetry code needs as input is *_INPUT.pdb. It is a monomer which is used in conjunction with the symmetry code to make the dimer.
In this case the cmd line should be:
docking_protocol.linuxgccrelease -database rosetta_database -s res.AB_0001_INPUT.pdb -nstruct 10 -ex1 -ex2
-out:file:fullatom -out:file:o res -symmetry:symmetry_definition symm.AB.def -symmetry:initialize_rigid_body_dofs
-symmetry:perturb_rigid_body_dofs 3 8″