Can one consider prepack before docking as a fast relax of subunits with backbone constraints?
If so, can one replace prepack step with a fast relax with backbone constraints of subunits?
Post Situation:
The hub for Rosetta modeling software
The prepack step exists to ensure that bad initial rotamers won't cause a minimization energy gradient that disfavors close contact, and ensures that all rotamers start in good states because packing occurs only at the (moving) interface. This prevents some trajectories for receiving better scores for having managed to repack bad rotamers far from the interface.
If you run fast relax before docking you do not need to prepack. You cannot use a command line flag to docking to replace prepack with fast relax; you probably could write a RosettaScript with that effect.