Fixed bb design with hydrogen bond constraint

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  • This topic has 6 replies, 2 voices, and was last updated 12 years ago by Anonymous.
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    • #1263
      Anonymous

        Hi,

        I want to know how can I define hydrogen bond constraint while doing a fixed bb design for my mutants. I rosetta to select only those residues from resfile that conform to the hydrogen bond constraint ??


        BHARAT

      • #7053
        Anonymous

          You should try defining your hydrogen bonds as AtomPairConstraints (http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/de/d50/constraint_file.html) and passing in a constraint weight/file with the flags

          -constraints:cst_fa_weight or -constraints:cst_weight
          and
          -constraints:cst_fa_file or -constraints:cst_file

          That said, I don’t think fixbb actually accepts constraints. Give this a shot. If it doesn’t work, I’ll see about adding a line of code to fixbb to tell it to use constraints (probably core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose() immediately after the scorefunction is defined). You’ll know if it works because constraint-related scorefunction terms will show up in your output score file.

        • #7055
          Anonymous

            Thank you for the advice. I will try it and report back to you…

          • #7057
            Anonymous

              Hi!!

              I have made the -constraints:cst_fa_file but what has to be done for -constraints:cst_fa ..

            • #7058
              Anonymous

                For -constraints:cst_fa_weight, pass a number weight for your constraint, based on how strong you want it to be. You can plot your constraint with a plotting program to see what scores it will have at what distances….or just give it a weight between 1 and 10 and not worry too much about it.

              • #7060
                Anonymous

                  Yes, you were right . The constraints does not work for fixbb design. So what has to be done next ??

                • #7061
                  Anonymous

                    I looked at fixing the fixbb application, but it turns out the better way to do this is via RosettaScripts. If you write yourself a simple script using ConstraintSetMover followed by PackRotamersMover it ought to work. (I’m not much good with RosettaScripts yet, so I can’t really help specifically). I’m told the “RosettaScripts” section of the manual is the best-documented part of the code and that you’ll have no problem writing yourself the script you’ll need: http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/

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