Using Rosetta Docking for nucleic acids

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    • April 28, 2011 at 1:16 pm #886
      Anonymous

        Hi,

        I tried to use RosettaDock with protein-nucleic acid chains. But I have a problem. Rosetta doesn’t seem to recognise nucleic acids with the parameters I used. Here is the error message:


        ERROR: unrecognized aa U
        ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 534

        The version of RosettaDock I compiled (3.2.1) worked with the protein-protein complexes I tried.

        I suppose there is a command to specify nucleic acids or a specific database to use. Can anybody please tell me how to use RosettaDock for protein-nucleic acid chains?

        Thanks in advance.

      • 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.

        • April 28, 2011 at 5:58 pm #5498
          Anonymous

            I’ve never done anything with RNA or DNA, but there’s a manual page about using RNA (http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/RNA_protein_changes.html), although it doesn’t seemed to be linked through the main documentation page. (But can be found by searching the online manual for “RNA”.)

          • August 8, 2011 at 12:01 pm #5942
            Anonymous

              I use RNA-protein complexes. I am reading the manual page about RNA. Thank you for the link. I will tell you if I have any trouble or solution.

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