Ligand docking cannot open the protein file

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    • October 17, 2017 at 3:17 pm #2755
      Anonymous

        Hi there!

        I follow the ligand docking tutorial from here: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial

        When I get to point 6 and try to run docking protocol via ./rosetta_scripts.linuxgccrelease @options it says ERROR: Cannot open file “3PBL_ETQ.pdb”

        How can I check the particular path to the file and correct, if needed?

        Thanks in advance!

         

      • October 17, 2017 at 4:03 pm #13818
        Anonymous

          It’s a bit hidden due to formatting issues, but the 3PBL_ETQ.pdb file is made in step 4.2, where you `cat` the cleaned 3PBL_A.pdb file with the ETQ.pdb file made in the molfile_to_params step.  — Were you able to get to this step, or was there a problem with an earlier step?

          If you have the 3PBL_ETQ.pdb file, but it’s not being found correctly, you can edit the `options` file, and give a full path to the file in the line with `-s`.

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