In the prepack folder after a successful docking2 run, I have three PDB files:
Why? Which one is the prepacked structure? And, why is prepack_score.sf empty?
SCORE: total_score description
SCORE: 0.000 proteins_0001
[All output files attached.]
Update: Did not realize this was a ROSIE run -- ROSIE is up-to-date. See below.
This was run on ROSIE dock2 . . .
For the prepack stage of ROSIE dock2, the 'proteins.pdb' file is the input structure, and the 'proteins_prepacked.pdb' is the output structure that's actually used for the following docking run. 'proteins.prepack.pdb' is a file that's being output as an intermediate by the prepacking protocol itself - for ROSIE dock2, it should be identical to the proteins_prepacked.pdb structure.
And the scorefile is empty because one of the last steps in the prepack protocol has a side effect of clearing out any of the scores in the Pose. It's not something to worry about.