high-res docking

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    • July 15, 2013 at 9:49 am #1658
      Anonymous

        Category:
        Docking
        Hello:
        After low-res docking,I’m going to do high-res protein/protein docking.There are two modes(High Resolution Docking Only;High Resolution Docking minimization)in the rosetta3.4 user guide.Which one should I choose?
        Here is my flags:
        1.High-res docking only flags
        -s 1.pdb

        -partners ABC_DE

        -ex1

        -ex2aro

        -use_input_sc

        -docking_local_refine

        -nstruct 1000

        -mute core.util.prof

        -out:overwrite

        -out:pdb

        -mute core.io.database

        2.High-res docking minimization flags
        -s 1.pdb

        -partners ABC_DE

        -ex1

        -ex2aro

        -use_input_sc

        -docking_local_refine

        -dock_min

        -nstruct 1000

        -mute core.util.prof

        -out:overwrite

        -out:pdb

        -mute core.io.database

        Thank you very much!

      • July 15, 2013 at 10:59 am #9048
        Anonymous

          Hi Tfliu!
          -dock_min flag does a single round of minimization in high resolution, skipping the mcm protocol. So if you want mcm protocol use the first set of flags.

        • July 16, 2013 at 2:39 am #9065
          Anonymous

            Thanks for kind comments!
            In the high-res docking,I use high-res docking only flags to repack sidechains followed by high-res docking minimization to minimize the energy of the rigid body position.Does this make sense?
            Also,is there something wrong with my high-res docking minimization flags?

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