How to prepare the pdblist file for docking_ensmble in Rosetta3.4

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  • This topic has 1 reply, 2 voices, and was last updated 9 years ago by Anonymous.
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    • June 2, 2015 at 2:27 am #2224
      Anonymous

        Did anyone do ensemble docking using rosetta3.4?
        I don’t know how to prepare those seemed like energy score(lowres_reference_energies_ , and highres_reference_energies_ from source code) at
        the end of pdblist file?

        An example of the pdblist is below:

        input/xxip01_0001.pdb.ppk
        input/xxip02_0001.pdb.ppk
        input/xxip03_0001.pdb.ppk
        input/xxip04_0001.pdb.ppk
        input/xxip05_0001.pdb.ppk
        input/xxip06_0001.pdb.ppk
        input/xxip07_0001.pdb.ppk
        input/xxip08_0001.pdb.ppk
        input/xxip09_0001.pdb.ppk
        input/xxip10_0001.pdb.ppk
        3.91556
        1.21555
        3.651
        5.58172
        5.10037
        0
        5.55114
        2.70723
        1.01661
        2.68865
        -53.1856
        -54.0107
        -50.6703
        -51.266
        -55.8924
        -55.34
        -53.3811
        -53.7216
        -49.4558
        -52.6443

      • July 3, 2015 at 7:58 pm #11075
        Anonymous

          From what I can tell, your interpretation of the format is correct.

          The file is usually created by the docking_prepack_protocol application during structure preparation. Just remember to pass the -docking:ensemble1 and -docking:ensemble2 options.

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