ERROR:: Can’t find starting structure: ../prepack/test.pdb

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    • April 24, 2008 at 2:25 pm #515
      Anonymous

        Hi,

        I have compiled 2.3.0 for linux 32/64 bits with both gnu compilers 3.4.6 and intel 9.1.
        I am now trying to verify the quality of the 4 executables produced.

        http://www.rosettacommons.org/tiki/tiki-index.php?page=Quick+Start

        ~> cd rosetta_documentation/docking/tutorial/examples/samplerun
        samplerun > rosetta.intel32-intel9-32bits.stripped aa test 1 -dock -s test -prepack_rtmin -quiet -ex1 -ex2aro_only -unboundrot
        fails with:
        …
        Atom_mode set to all
        [STR OPT]Default value for [-paircutoffs] paircutoffs.
        Reading ../../../../../rosetta_database/paircutoffs
        [T/F OPT]Default FALSE value for [-interface_ds]
        [T/F OPT]Default FALSE value for [-decoystats]
        set_decoystats_flag: from,to F F
        [T/F OPT]Default FALSE value for [-decoyfeatures]
        [T/F OPT]Default FALSE value for [-t32s3]
        [T/F OPT]Default FALSE value for [-evolution]
        [T/F OPT]Default FALSE value for [-evol_recomb]
        [T/F OPT]Default FALSE value for [-profile]
        [T/F OPT]Default FALSE value for [-dummy_model]
        [T/F OPT]Default FALSE value for [-saxs_model]
        Profile defined from q = 0 to 1.
        Searching for dat file: ./test.dat
        Searching for dat file: ./test.dat
        WARNING!! .dat file not found!
        Looking for fasta file: ./test1.fasta
        fasta file not found!
        setup_protein_sstype: query sequence not defined !!!
        fasta file needed to read in psipred prediction !!!
        query sstype will not be defined in this run !!!
        ERROR:: Can’t find starting structure: ../prepack/test.pdb
        ERROR:: Exit from: input_pdb.cc line: 3028

        there seems to be missing the ../prepack directory

        Any idea?

        Tru

      • April 28, 2008 at 2:17 pm #3935
        Anonymous

          You need supply a path file named “path.txt” in your current directory or use flag “-path xxx/xxx” to tell rosetta where the file is. This file specifies the input/output file paths, the database and score output paths. The error you mentions is because that rosetta could not find the input file in the directory as the definition path.txt.
          For more details, please check the README.paths.txt

          > Hi,
          >
          > I have compiled 2.3.0 for linux 32/64 bits with both gnu compilers 3.4.6 and intel 9.1.
          > I am now trying to verify the quality of the 4 executables produced.
          >
          > http://www.rosettacommons.org/tiki/tiki-index.php?page=Quick+Start
          >
          > ~> cd rosetta_documentation/docking/tutorial/examples/samplerun
          > samplerun > rosetta.intel32-intel9-32bits.stripped aa test 1 -dock -s test -prepack_rtmin -quiet -ex1 -ex2aro_only -unboundrot
          > fails with:
          > …
          > Atom_mode set to all
          > [STR OPT]Default value for [-paircutoffs] paircutoffs.
          > Reading ../../../../../rosetta_database/paircutoffs
          > [T/F OPT]Default FALSE value for [-interface_ds]
          > [T/F OPT]Default FALSE value for [-decoystats]
          > set_decoystats_flag: from,to F F
          > [T/F OPT]Default FALSE value for [-decoyfeatures]
          > [T/F OPT]Default FALSE value for [-t32s3]
          > [T/F OPT]Default FALSE value for [-evolution]
          > [T/F OPT]Default FALSE value for [-evol_recomb]
          > [T/F OPT]Default FALSE value for [-profile]
          > [T/F OPT]Default FALSE value for [-dummy_model]
          > [T/F OPT]Default FALSE value for [-saxs_model]
          > Profile defined from q = 0 to 1.
          > Searching for dat file: ./test.dat
          > Searching for dat file: ./test.dat
          > WARNING!! .dat file not found!
          > Looking for fasta file: ./test1.fasta
          > fasta file not found!
          > setup_protein_sstype: query sequence not defined !!!
          > fasta file needed to read in psipred prediction !!!
          > query sstype will not be defined in this run !!!
          > ERROR:: Can’t find starting structure: ../prepack/test.pdb
          > ERROR:: Exit from: input_pdb.cc line: 3028
          >
          > there seems to be missing the ../prepack directory
          >
          > Any idea?
          >
          > Tru

        • April 28, 2008 at 5:35 pm #3937
          Anonymous

            > You need supply a path file named “path.txt” in your current directory or use flag “-path xxx/xxx” to tell rosetta where the file is. This file specifies the input/output file paths, the database and score output paths. The error you mentions is because that rosetta could not find the input file in the directory as the definition path.txt.
            > For more details, please check the README.paths.txt

            you mean “paths.txt” ?

            there is one there (the one provided by the rosetta_documentation tar.gz file)
            The only modification I did was to change the data files to:
            ../../../../../rosetta_database/ (as stated in the Quick+Start page).

            the full “paths.txt” file is as follow:
            Rosetta Input/Output Paths (order essential)
            path is first ‘/’, ‘./’,or ‘../’ to next whitespace, must end with ‘/’
            INPUT PATHS:
            native structure(required) ../
            unbound structure(optional) ../
            alternate data files(optional) ./
            fragments(not used) ./
            structure dssp (not used) ./
            sequence map(optional) ./
            constraints(optional) ../
            starting structure(required) ../prepack/
            data files(required) ../../../../../rosetta_database/
            OUTPUT PATHS:
            movie ./
            pdb path ./
            score ./
            status ./
            user ./
            FRAGMENTS: (use ‘*****’ in place of pdb name and chain)
            2 number of valid fragment files
            3 frag file 1 size
            aa*****03_05.200_v1_3 name
            9 frag file 2 size
            aa*****09_05.200_v1_3 name

            The issue I have is that the “required” data files (in ../prepack) are not provided and I have no
            idea how to generate one (basic beginner question).

            Thanks.

            Tru

          • May 7, 2008 at 5:50 pm #3947
            Anonymous

              …
              >
              > The issue I have is that the “required” data files (in ../prepack) are not provided and I have no
              > idea how to generate one (basic beginner question).
              > …

              Anyone? Am I the only one having this problem?

            • May 7, 2008 at 6:46 pm #3948
              Anonymous

                You have to have a sequence(fasta) file for docking simulations. which should in the dat directory.
                http://www.rosettacommons.org/tiki/tiki-index.php?page=File+Format#Sequences_FASTA_

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