rosetta protein protein docking start up

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    • June 24, 2011 at 4:01 pm #960
      Anonymous

        Hi all

        I just tried to install Rosetta 3.2.1 X64 bit in Redhat linux, guessing managed to install the software after initial trouble.
        But do not know how to proceed to for doing docking and other usage of software. I did gone through the guide but not
        clear enough for me.

        Please how can I set up the environment and run either command mode or graphical interface of Rosetta for docking and other
        calculations.

        I did see some script on the website but not clear information for the beginner to initiate the start up, Is there any step by step procedure or script that can be useful for docking and other calculations.

        Any help could be appreciated
        thanksv

      • June 24, 2011 at 5:04 pm #5813
        Anonymous

          After you build the applications by issuing ./scons.py -jN mode=release bin from the rosetta directory, you should find all of the executables in the rosetta/bin directory. The executables generally have descriptive names. To run docking, execute the “docking_protocol.[OS_TYPE][COMPILER][MODE]” (e.g. docking_protocol.linuxgccrelease) executable. The documentation pages should provide you with commonly used flags to give you additional guidance you need. The documentation for docking can be found here: http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_docking.html

        • June 24, 2011 at 6:53 pm #5816
          Anonymous

            Dear Wieztner, Thanks a lot.

            I want to dock model_2.pdb on compx.pdb (fixed),

            I did run the following commands,

            ~/Downloads/ros1/rosetta_source/bin/docking_protocol.linuxgccrelease -database /home/Downloads/ros1/rosetta_database -s ../../pdb/model_2.pdb compx.pdb

            Got the following error message ?

            protocols.jd2.PDBJobInputter: filling pose from PDB ../../pdb/model_2.pdb
            protocols.docking.DockingProtocol: Setting docking foldtree
            protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 98 -1
            protocols.docking.DockingProtocol:

            ERROR: cutpoint
            ERROR:: Exit from: src/protocols/docking/util.cc line: 91
            > ~/Downloads/ros1/rosetta_source/bin/docking_protocol.linuxgccrelease -database /home/Downloads/ros1/rosetta_database -s ../../pdb/model_2.pdb compx.pdb

            any help? Thanks.

          • July 1, 2011 at 9:38 pm #5828
            Anonymous

              Dear Lewis,

              Thanks a lot, it works fine. But want to know how can I do multiple docking?, rosetta docking gave me one solution. Also I do have model for one monomer , like to do oligomer assembly, how can I increase the probability for different orientation of the molecule. I do have a homomeric receptor and ligand as one model, like to do the docking for heteomeric assembly for example (tetramer of receptor and wants to dock one model with different oligomeric state.

              Is it possible?

              thanks a lot

            • July 1, 2011 at 2:15 pm #5827
              Anonymous

                I’m pretty sure that docking needs the two proteins to be in the same input PDB. They can be separated by 100 angstroms or whatever, but they need to be in the same file (with different chain letters).

              • July 2, 2011 at 7:42 pm #5829
                Anonymous

                  There is a flag that lets you control which groups of chains form rigid units. With a monomer, chain A, docking to a tetramer, chains BCDE, you’d use “-partners A_BCDE” to keep the tetramer internally rigid.

                  There is no way to dock three or more moving bodies at a time that I know of.

                  I’m not sure I’ve answered your question – does this cover it?

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