Reply To: Using Rosetta Docking for nucleic acids

Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Using Rosetta Docking for nucleic acids › Reply To: Using Rosetta Docking for nucleic acids

April 28, 2011 at 2:51 pm #5497
Anonymous

    U is an RNA nucleic acid. Non-RNA Rosetta executeables recognize only DNA by default, because the DNA and RNA names conflict, and the authors decided to offer one-or-the-other instead of figuring out a system for both. Are you doing RNA-protein complexes or DNA-protein complexes?

    If this is not the problem it’s probably a nomenclature thing. Your residue names need to match what Rosetta has in its parameter files in the database (database/chemical/residue_type_sets/fa_standard/ or something like that). Note that the RNA is NOT in the fa_standard set, but DNA is. If you’re using DNA I can help you debug this path.