-loops:fa_input not found in command line top-level context

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    • August 24, 2017 at 10:15 am #2726
      Anonymous

        Hi everybody!

        I’m trying to learn how to use Rosetta in de novo protein design. I use this article as a manual: https://www.ncbi.nlm.nih.gov/pubmed/23744289

        It doesn’t work for me at some point. Namely, when I go to step 13 (Running the comparative modeling job), I try to execute the following command in the terminal:

        ./loopmodel.default.linuxgccrelease @modeling.options -database rosetta_database -nstruct 100

        But the response is:

        ERROR: ERROR: Option matching -loops:fa_input not found in command line top-level context

        It seems rather strange, because Rosetta modeling option contains the description of this parameter: https://www.rosettacommons.org/manuals/rosetta3.1_user_guide/opt_loops.html

        My rosetta version is rosetta_bin_linux_2017.08.59291_bundle

        I performed search of this error on the forum but didn’t find anything.

         

        Thank you in advance!

        Nick.

      • August 24, 2017 at 3:09 pm #13707
        Anonymous

          The documentation page you’re looking at is for Rosetta 3.1, which is old (released late 2009). The manual for recent versions of Rosetta can be found here: https://www.rosettacommons.org/docs/latest/Home

          That particular option (-loops:fa_input) hasn’t been used in a while. I don’t belive it’s necessary for most current loop modeling applications. In a pinch you can try ‘-in:file:fullatom’ to tell Rosetta that your input structures are in fullatom format, but that’s likely not going to be necessary.

          • August 25, 2017 at 12:08 pm #13713
            Anonymous

              Thank you very much for the link!

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