Reply To: Symmetric local protein docking

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January 12, 2011 at 8:13 am #4816
Anonymous

    Thanks a lot for the quick reply.
    I tried your suggestion and got a different error when running docking_protocol.linuxgccrelease.

    Here is the error:
    protocols.docking.DockingProtocol: Setting docking foldtree
    protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 126 -1
    protocols.docking.DockingProtocol:
    ERROR: cutpoint
    ERROR:: Exit from: src/protocols/docking/DockingProtocol.cc line: 284

    My steps were:
    1) I have a model of a trimer that I want to refine.
    I deleted one of the monomers and saved the remaining 2 monomers (chains A and B) in a pdb file.
    2) I ran prepacking by:
    docking_protocol.linuxgccrelease -database rosetta_database -s res.AB.pdb -docking:dock_ppk
    3) I prepared the symmetry definition file by:
    make_symmdef_file.pl -m NCS -a A -i B -r 12.0 -p res.AB_0001.pdb > ! symm.AB.def
    4) I ran rosettaDock by:
    docking_protocol.linuxgccrelease -database rosetta_database -s res.AB_0001_INPUT.pdb -nstruct 1 -ex1 -ex2 -out:file:fullatom -out:file:o res -symmetry:symmetry_definition symm.AB.def -symmetry:initialize_rigid_body_dofs -symmetry:perturb_rigid_body_dofs 3 8

    Thanks,
    Efrat.