Can one use a non-write privileged rosetta executable?

Member Site Forums Rosetta 3 Rosetta 3 – Build/Install Can one use a non-write privileged rosetta executable?

  • This topic has 5 replies, 2 voices, and was last updated 12 years ago by Anonymous.
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    • #1106

        I am trying to do a comparative modelling using /sware/rosetta3.3/linux/rosetta_source/bin/minirosetta.linuxgccrelease.
        The program didn’t run, and the last few lines of the log file are:

        Warning: Unable to locate database file Dunbrack02.lib.bin
        core.pack.dunbrack: Dunbrack library took 8.4 seconds to load from ASCII
        Warning: Unable to locate database file Dunbrack02.lib.bin
        Warning: Unable to locate database file Dunbrack02.lib.bin
        core.pack.dunbrack: Opening file /sware/rosetta3.3/linux/rosetta_database/dun02bwtPgW for output.
        core.pack.dunbrack: Unable to open temporary file in rosetta database for writing the binary version of the Dunbrack02 library.
        core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
        core.pack.pack_rotamers: built 11 rotamers at 1 positions.
        core.pack.pack_rotamers: IG: 492 bytes
        protocols.jd2.JobDistributor: no more batches to process…
        protocols.jd2.JobDistributor: 0 jobs considered, 0 jobs attempted in 0 seconds
        protocols.jd2.JobDistributor: no jobs were attempted, did you forget to pass -overwrite?

        I noticed on a previous post for someone with a related problem that smlewis suggested to check that
        the Rosetta executable has write permissions to the database directory. Currently, the Rosetta that I am using
        is on a shared (multi-user)system, and the computer manager does not want to give the executable write
        privileges in such a case. He suggested that I download Rosetta into my personal directory. Is that the only fix?

        Thanks, -Jerry

      • #6350

          If you don’t have write permission to the database, then Rosetta will work in most cases, but you’ll have to do a slow initialization step (the Dunbrack library) every time. It’ll add maybe 30 seconds every time you run rosetta.

          I don’t have enough information to diagnose why it didn’t run. Is the output already present (in which case you need -overwrite)? Do you have write permissions in the directory you are running Rosetta in?

        • #6354

            I do have write permissions in the directory I am running Rosetta in.
            I also tried running the program using the command:
            /sware/rosetta3.3/linux/rosetta_source/bin/minirosetta.linuxgccrelease @Tm7_39.options -overwrite true
            and again with “-out:overwrite true” in the options file, but either way got the same log file result as previously.


            Forgive my inexperience, but in order to do a slow initialization step (the Dunbrack library),
            what specific command should I give?
            and where exactly do I put it? (i.e. in the options file?).


            FYI, the options file I am curently using is:
            -run:protocol threading
            -in:file:fasta Tm7_39.fasta
            -out:overwrite true
            -loops:frag_files aat000_09_05.200_v1_3 aat000_03_05.200_v1_3 none
            -loops:frag_sizes 9 3 1
            -in:file:native 1IC2CD7_39.pdb
            -idealize_after_loop_close #Idealize structure after closing loops
            -loops:remodel quick_ccd

            -loops:relax fastrelax

            -in:file:alignment Tm7_39_2zta.ali #Alignment file (?with>for multiple chains?)

            -cm:aln_format grishin #Alignment file format

            -in:file:template_pdb 2ZTAnoHET.pdb #Template PDBs ? whether to clean it first

            -database /sware/rosetta3.3/linux/rosetta_database #Path to database

            -out:nstruct 1 # #models to build, increase to 1000 when works

            -nstruct 1 #Number of output structures Later increase to 1000

            -out:pdb #Use PDB file output, default=false

            -out:path . #Path where PDB output files will be written, default ‘.’


            Thanks again so much,

          • #6357

              I’ve been trying a lot of different things, but still can’t get the comparative modeling to run. I’ve been basing my commands on that found in

              Are there any bugs here that I should know about?
              For example, when I include the command -relax:fastrelax_repeats 8, I get an error:
              “Option matching -relax:fastrelax_repeats not found in command line top-level context”

              Also, my alignment is very obvious, but the “grishin” format is not clearly described: e.g., what are the 2 and 9 before the sequences?

              Thanks, -Jerry

            • #6356

                The Dunbrack library binary file (which you cannot write) initializes itself as needed. The fact that you can’t write it just means Rosetta will try to write it fruitlessly once per executable.

                I don’t know why you get no output from the data I have. I will guess that something is screwy in your alignment setup (the alignment file vs the template file have different tags for the PDB or something…..?)

              • #6358

                  Maybe this will help with the grishin format?


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