docking_prepack_protocol generates several output pdb structures:
where * stands for the name of the crystal structure that was given as input to docking_prepack_protocol.
What are the differences between these .pdb files that docking_prepack_protocol outputs?
From what I've inferred so far, the away_*.pdb files contain the partners separated in space, with away_packed_*.pdb containing the packed rotamers I presume. Then the partners are brought back together, and they are together in initial__*_0001.pdb, prepack__*_0001.pdb and *_0001.pdb. Which of these last three should I send to docking_protocol?