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

[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