Protein Docking Error

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    • August 17, 2017 at 9:57 am #2718
      Anonymous

        Dear All,

         

        I am learning how to do protein-ligand docking and I am following the Rosetta built-in tutorial: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial

         

        I did not change anything whatsoever. I used the same tutorial files (as is) and attempted to run the calculation as such:

        {PATH_TO_ROSETTA}/main/source/bin/rosetta_scripts.linuxgccrelease @options

         

        But i keep getting an ERROR message regarding LigandArea (log file attached).

         

        Has something changed at some point in the Rosetta releases? How to fix this error?

      • August 17, 2017 at 8:54 pm #13676
        Anonymous

          We changed the format for RosettaScripts XML between Rosetta 3.7 and 3.8. The issue is that you have a Rosetta-3.8 style XML, but are attempting to use it with Rosetta 3.7. 

          I’d recommend using this XML with Rosetta 3.8 (or a recent weekly), or if you do want to use Rosetta 3.7 for some reason, take a look at the demos which came with Rosetta 3.7 for an example of the format of the XML to use.

          (If you were going the other way – that is, attempting to use an old XML with a newer Rosetta, I’d tell you to use the conversion script, but we don’t have a conversion script to go “backwards” — you’d have to find some other workaround.)

        • August 18, 2017 at 7:53 am #13681
          Anonymous

            I understand,

             

            I compiled rosetta 3.8 and you are right, the script works fine.

             

            Thanks

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