Reply To: low resolution blind protein-protein docking with a ligand

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March 21, 2011 at 6:03 pm #5218
Anonymous

    We did inadvertently compile in debug mode [this is was the first time we’d ever built Rosetta] & were so anxious to use it, that we left it at that rather than do it again. It may be time to redo & update while we’re at it.

    Yes, you did help us get to a centroid heme. Here are the flags we’re using:
    @localhost lores-hem]$ cat flags
    -in
    -file
    -s cytHNbHEx.pdb
    # the input file should have two single, complete chains A and B
    # for Ab molecules (with L+H chains) use -docking::partners flag below
    -path
    -database /opt/rosetta/rosetta_database/
    # customize this to point to your installation directory
    -extra_res_fa /home/newhojs/Desktop/RosettaParams/HEC.params /home/newhojs/Desktop/RosettaParams/HEM.params
    -extra_res_cen /home/newhojs/Desktop/RosettaParams/loresHEx/HEC.cen.params /home/newhojs/Desktop/RosettaParams/loresHEx/HEM.cen.params
    -docking
    -randomize1
    # rotates partner1 (chain A) before docking proteins together
    #-randomize2
    # rotates partner2 (chain B) before docking proteins together
    -partners AD_BE
    # defines docking partners by ChainID; see manual
    -out
    -nstruct 1000
    # this should be set to a large number for effective sampling
    -mute core.util.prof
    # reduces copious output, without overdoing as with -mute all
    -file
    -o dock_output
    # scorefile will be named dock_output.sc (or .fasc for fullatom)
    #-fullatom
    # fullatom is commented out for fast low-res "centroid mode" run
     I don’t think we’re using full-atom mode. I can’t really attach the log file because it’s over 1MB & I’d prefer to compress it, but compressed file extensions aren’t supported by the forum software. So I grepped: $ grep -n pack *.log
    7:core.io.database: Database file opened: /opt/rosetta/rosetta_database/cenpack_log.txt
    279:core.pack.task: Packer task: initialize from command line()
    535:core.pack.task: Packer task: initialize from command line()
    552:core.io.database: Database file opened: /opt/rosetta/rosetta_database/cenpack_log.txt
    When I tail the log file: tail *.log
    protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822 72.6401 -22.8441 -11.3836
    protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822 71.6688 -22.6469 -11.2505
    protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822 71.6688 -22.6469 -11.2505
    protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822 70.6975 -22.4497 -11.1174
    protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822 70.6975 -22.4497 -11.1174
    protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822 69.7263 -22.2526 -10.9843
    protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822 69.7263 -22.2526 -10.9843
    protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822 68.755 -22.0554 -10.8511
    protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822 68.755 -22.0554 -10.8511
    protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.636906 -0.754867 -0.156607 0.765473 0.595051 0.24488 -0.0916633 -0.275844 0.956822

    It trails off because we killed the job. There are a LOT of lines that resemble this one in the log file…

    Thanks for your help!