capping termini

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    • May 12, 2008 at 5:50 pm #551
      Firas Khatib
      Participant

        Hi,

        The structures that I’m generating with Rosetta are missing the hydroxyl group at the C terminus. I’m guessing this is because the residues are generated without them so that they can be connected to one another, but this is creating problems for me when I try to analyze the generated structures.

        How can I run Rosetta in a way that will cap the C terminus correctly? Is there a specific option? Or a separate command? Here’s the main command in what I’m running:

        “rosetta aa inpu _ -relax -farlx -termini -minimize -s highRes -fa_input -fa_output > refine.log”

        When I look at files from the PDB, they have something similar to this line at the C terminus, which is the OH group:
        “ATOM 2590 OXT SER B 416 48.151 19.779 122.824 1.00107.18 O”

        Any help would be greatly appreciated; thanks!

        Anna

      • May 12, 2008 at 6:53 pm #3962
        Anonymous

          Can you try to use the flag “-termini ” which invoke the modeling of both N and C termini. Or the flag “-Cterminus” which invoke the modeling of C termini residue only.

          Please let me know whether this works since I never use them myself.

          Yi

          > Hi,
          >
          > The structures that I’m generating with Rosetta are missing the hydroxyl group at the C terminus. I’m guessing this is because the residues are generated without them so that they can be connected to one another, but this is creating problems for me when I try to analyze the generated structures.
          >
          > How can I run Rosetta in a way that will cap the C terminus correctly? Is there a specific option? Or a separate command? Here’s the main command in what I’m running:
          >
          > “rosetta aa inpu _ -relax -farlx -termini -minimize -s highRes -fa_input -fa_output > refine.log”
          >
          > When I look at files from the PDB, they have something similar to this line at the C terminus, which is the OH group:
          > “ATOM 2590 OXT SER B 416 48.151 19.779 122.824 1.00107.18 O”
          >
          > Any help would be greatly appreciated; thanks!
          >
          > Anna

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