I followed pyrosetta tutorials for docking. I did something like the following:
scorefxn_low = create_score_function("interchain_cen")
jd = PyJobDistributor("output", 100, scorefxn_low) while not jd.job_complete: cen_pose.assign(starting_cen_pose) dock_lowres.apply(cen_pose) jd.output_decoy(cen_pose)
Then, I selected the candiddate with lowest score.
Now, my question is how can I add my own constraints (I have some constraints between CB of residues of chains A and B). I know how to add constraints, but I don't know which part of the above code (or code in toturial for docking) must be changeed in order to include my constraints.