the output of ligand docking

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    • July 3, 2015 at 8:27 am #2221
      Anonymous

        Dear all,
        I run the ligand docking protocol to dock a small chemical to protein.
        this is my flag
        -packing
        -no_optH
        -ex1
        -ex1aro
        -ex2
        -docking
        -dock_pert 30 5
        -ligand
        -improve_orientation 1000
        -minimize_ligand
        -harmonic_torsions 10
        -minimize_backbone
        -harmonic_Calphas 0.3
        -soft_rep
        -old_estat
        -start_from 1.36 50.07 23.4
        -protocol abbrev2

        When I take a look on the output files, I saw the lowest score out files of this run is far away together (up to 25 Angstrom). Is it normal? If it is normal, Can I say the chamical was moved around my protein?
        As I expected the output will local in the sphere with dimeter about 10Anstrong.

        Could some one help me?

        Thank in advance and best regards
        Phan Vy

      • July 3, 2015 at 8:14 pm #11079
        Anonymous

          This is more or less the same question as https://www.rosettacommons.org/node/9459 right? Or is there some subtle aspect I’m missing? (I’ll admit I don’t understand what you mean by “far away together”.)

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