Modeling flexible linkers with Floppytail

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    • May 12, 2013 at 10:55 pm #1577
      Anonymous

        Hi, I am modeling linkers between domains in a protein. I am using FloppyTail application in Rosetta 3.4.
        I had a couple of questions to make sure I am using correct options.

        Is there an example of options for this case?
        Should I be specifying AnchoredDesign options?
        what is the difference between FloppyTail.default.linuxgccrelease and FloppyTail.linuxgccrelease?
        Can I run this application with mpi?

        For now my flags look like this:

        -database /rosetta/rosetta3.4/rosetta_database/
        -in:file:s inputfile.pdb
        -in:file:movemap linksfile
        -nstruct 30000

        Thank you for any suggestions and recommendations.

      • May 27, 2013 at 8:15 am #8829
        Anonymous

          hi pdbb,
          These links might help:

          https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d8/d39/_floppy_tail.html
          https://www.rosettacommons.org/node/2358

          compile with mpi option to get FloppyTail.mpi.linuxgccrelease
          $ ./scons.py bin mode=release extra=mpi

        • September 22, 2013 at 9:14 pm #9317
          Anonymous

            Is there an example of options for this case?

            Yes, in the demo in the rosetta_demos folder.

            Should I be specifying AnchoredDesign options?

            In 3.4, yes; in the most recent release (week 38 weekly release), no

            what is the difference between FloppyTail.default.linuxgccrelease and FloppyTail.linuxgccrelease?

            “default” is guaranteed to have no extra compiler options like mpi. The one without default is whatever you’ve compiled most recently. If you’ve compiled in both MPI and not MPI, you’ll have:

            FloppyTail.default.linuxgccrelease
            FloppyTail.mpi.linuxgccrelease
            FloppyTail.linuxgccrelease

            The last one will point to whatever you compiled most recently.

            Can I run this application with mpi?

            Sure – just compile in MPI with “extras=mpi” when you compile.

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