how to add water into protein interface using solvated rotamers?

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    • July 22, 2013 at 3:25 am #1669
      Anonymous

        Hello,

        Im new to Rosetta. Im trying the tutorials of PyRosetta, but I couldn’t find any clues that could help me add water into the protein interfaces using the Solvated Rotamers (as stated in the paper by Jiang et al. 2005 “A solvated rotamer” approach to modeling water-mediated hydrogen bonds at protein-protein interfaces).

        Anyone please suggests me any hint or readings that I can find how to do it!

        Thank you very much.

        Regards,
        chinh

      • July 28, 2013 at 9:29 pm #9146
        Anonymous

          This work was done in “old Rosetta” (Rosetta++). (Note the date on the paper). PyRosetta is based on Rosetta3, which was a total rewrite of Rosetta++. I don’t think that the solvated rotamer code was ported, and so I don’t think it works at all in current Rosetta or PyRosetta. I found the options to turn it on (-packing:explicit_h2o or -packing:solvate) but they are not hooked up to any code.

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