Output structures from docking_prepack_protocol: initial__*.pdb vs prepack__*.pdb, which one should I send to docking_protocol?

[Anonymous]

docking_prepack_protocol generates several output pdb structures:

away__*_0001.pdb
away_packed__*_0001.pdb
initial__*_0001.pdb
prepack__*_0001.pdb
*_0001.pdb

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?

Thanks.

[Anonymous]

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.

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