Script not working

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    • June 12, 2013 at 11:38 am #1610
      Anonymous

        Dear friends
        i am trying to run script “clean_pdb.py” but its not running and showing error massage….
        how can i come out of it.. Please help

        zebrafish@ubuntu:~/rosII/rosetta-3.5/rosetta_demos/public/dock_ligand_and_proteins/scripts$ python clean_pdb.py
        Traceback (most recent call last):
        File “clean_pdb.py”, line 11, in
        from amino_acids import longer_names
        ImportError: No module named amino_acids
        zebrafish@ubuntu:~/rosII/rosetta-3.5/rosetta_demos/public/dock_ligand_and_proteins/scripts$

      • June 12, 2013 at 6:23 pm #8892
        Anonymous

          The amino_acids.py module is in rosetta_source/src/python/apps/public/

          If you copy or link that file to the rosetta_demos/public/dock_ligand_and_proteins/scripts/ directory, the clean_pdb.py script should work.

        • June 13, 2013 at 7:01 am #8894
          Anonymous

            One more problem i am facing is that when i am running “molfile_to_params.py -c -n RAP rap.mol” its generating RAP.fa.params RAP.cen.params but not generating the RAP.params file for my lingand. Even more same thing happening with other ligads also … :(

            output of given command:


            zebrafish@ubuntu:~/rosII/rosetta-3.5/rosetta_demos/public/dock_ligand_and_proteins/Part1$ /home/zebrafish/rosII/rosetta-3.5/rosetta_source/src/python/apps/public/molfile_to_params.py -c -n RAP rap.mol
            Centering ligands at ( -8.689, 26.857, 36.818)
            Atom names contain duplications — renaming all atoms.
            Total naive charge -5.315, desired charge 0.000, offsetting all atoms by 0.033
            WARNING: fragment 1 has 162 total atoms including H; protein residues have 7 – 24 (DNA: 33)
            WARNING: fragment 1 has 65 non-H atoms; protein residues have 4 – 14 (DNA: 22)
            WARNING: fragment 1 has 14 rotatable bonds; protein residues have 0 – 4
            Average 162.0 atoms (65.0 non-H atoms) per fragment
            (Proteins average 15.5 atoms (7.8 non-H atoms) per residue)
            WARNING: no root atom specified, using auto-selected NBR atom instead.
            WARNING: skipping extra samples for proton chis; would give 43046721 conformers
            Wrote params file RAP.fa.params
            Wrote PDB file RAP_0001.fa.pdb
            WARNING: skipping extra samples for proton chis; would give 43046721 conformers
            Wrote params file RAP.cen.params
            Wrote PDB file RAP_0001.cen.pdb

          • June 18, 2013 at 5:57 am #8911
            Anonymous

              Thanks for your valuable reply. :)

            • June 18, 2013 at 10:06 am #8912
              Anonymous

                Hii, i stucked again while running the demo file the ligand docking protocal (/rosetta-3.5/rosetta_demos/public/dock_ligand_and_proteins)”, this time ERROR related to mover its showing

                “Error: ERROR: Exception caught by JobDistributor while trying to get pose from job FKBP+RAP_0001’SlideTogether’ mover requires chains tag” output showing bellow:
                ===========================================================================================================================================================

                setting ligand_soft_rep weight hack_elec to 0.42
                defined score function “hard_rep” with weights “ligand”
                setting hard_rep weight hack_elec to 0.42
                protocols.jd2.DockDesignParser: Defined mover named “translate” of type Translate
                protocols.jd2.DockDesignParser: Defined mover named “rotate” of type Rotate
                Error: ERROR: Exception caught by JobDistributor while trying to get pose from job FKBP+RAP_0001’SlideTogether’ mover requires chains tag
                Error:
                Error: Treating failure as bad input; canceling similar jobs
                protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: FKBP+RAP_0001
                protocols.jd2.JobDistributor: no more batches to process…
                protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 4 seconds
                zebrafish@ubuntu:~/

              • July 1, 2013 at 8:39 am #8979
                Anonymous

                  thanks ………. its working now

                • June 13, 2013 at 5:21 am #8893
                  Anonymous

                    Its working now
                    thaaaaaaaaaaaaaaaaaaanks a lot :)

                  • June 13, 2013 at 5:49 pm #8896
                    Anonymous

                      The RAP.fa.params file *is* the RAP.params file you get normally. It’s entirely identical. It’s just named differently so you don’t accidentally confuse the full atom params file with the centroid one you’ve also generated.

                    • June 18, 2013 at 5:54 pm #8915
                      Anonymous

                        The interface to the SlideTogether mover changed from when the demo was written to when 3.5 was released.

                        Instead of taking just a single chain, the SlideTogether mover now takes a list of chains, comma seperated. Just change “chain=X” to “chains=X” in dock_ligand_and_proteins/Part2/ligand_dock.xml and it should work.

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