docking2: will the real prepacked PDB stand up?

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    • February 21, 2017 at 6:04 pm #2588
      Anonymous

        In the prepack folder after a successful docking2 run, I have three PDB files:

        proteins_prepacked.pdb

        proteins.pdb

        proteins.prepack.pdb

        Why? Which one is the prepacked structure? And, why is prepack_score.sf empty?

        SEQUENCE: 

        SCORE: total_score description 

        SCORE:       0.000 proteins_0001

        [All output files attached.]

      • February 25, 2017 at 3:39 pm #12158
        Anonymous

          This was run on ROSIE dock2 . . .

        • February 25, 2017 at 3:39 pm #12679
          Anonymous

            This was run on ROSIE dock2 . . .

          • February 25, 2017 at 3:39 pm #13200
            Anonymous

              This was run on ROSIE dock2 . . .

            • February 28, 2017 at 11:45 pm #12154
              Anonymous

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

              • February 28, 2017 at 11:45 pm #12675
                Anonymous

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

                • February 28, 2017 at 11:45 pm #13196
                  Anonymous

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

                  • February 28, 2017 at 4:34 pm #12164
                    Anonymous

                      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.

                       

                       

                    • February 28, 2017 at 4:34 pm #12685
                      Anonymous

                        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.

                         

                         

                      • February 28, 2017 at 4:34 pm #13206
                        Anonymous

                          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.

                           

                           

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