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?
The different outputs reflect the state of the protein at different points in the prepack protocol. Basically, the prepack protocol takes a complex, separates the subunits, repacks them in the separated state, and then translates them back together again.
initial – the protein after being loaded and being setup
away – the protein after the subunit have been translated away from each other
away_packed – the protein after the subunits have been repacked in the separated state
prepack – the protein after having been back together again, after being repacked in the separated state.
*_0001.pdb – the standard Rosetta output. This should be more-or-less equivalent to the prepack structure.
You can use either the prepack or the plain *_0001.pdb structure as the input for your docking protocol.