model protein at low pH

Member Site › Forums › Rosetta 3 › Rosetta 3 – General › model protein at low pH

  • This topic has 1 reply, 2 voices, and was last updated 12 years ago by Anonymous.
Viewing 1 reply thread
  • Author
    Posts
    • November 5, 2012 at 3:52 pm #1452
      Anonymous

        Hi,

        I’m a noob in rosetta modelling. I need to model my protein at low pH, i.e. with protonated Asp and Glu residues. How should I setup the simulation(ab initio and relax)?

        I found there are residue type files for fullatom protonated Asp and Glu in rosetta_source directory, but I don’t know how to use them:(

        Thank you very much,

        Yisong

      • November 5, 2012 at 4:23 pm #8024
        Anonymous

          There are two flags one can add to activate those protonation states. It is unclear what changes need to be made to the scorefunction in general (I mean the science is unclear), so it’s pretty experimental. Please see this post: http://www.rosettacommons.org/content/mitochondria-protein-modeling#comment-5435

      • Author
        Posts
      Viewing 1 reply thread
      • You must be logged in to reply to this topic.