the output of ligand docking

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    • #2221

        Dear all,
        I run the ligand docking protocol to dock a small chemical to protein.
        this is my flag
        -dock_pert 30 5
        -improve_orientation 1000
        -harmonic_torsions 10
        -harmonic_Calphas 0.3
        -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

      • #11079

          This is more or less the same question as 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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