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docking2: will the real prepacked PDB stand up?

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docking2: will the real prepacked PDB stand up?

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.]

proteins.prepack.pdb459.98 KB
proteins.pdb466.57 KB
proteins_prepacked.pdb459.98 KB
Post Situation: 
Tue, 2017-02-21 10:04
David Weis

Update: Did not realize this was a ROSIE run -- ROSIE is up-to-date. See below.

Tue, 2017-02-28 15:45

This was run on ROSIE dock2 . . .

Sat, 2017-02-25 07:39
David Weis

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.



Tue, 2017-02-28 08:34