Can one use a non-write privileged rosetta executable?

This topic has 5 replies, 2 voices, and was last updated 13 years ago by Anonymous.

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- November 29, 2011 at 8:15 pm #1106
  Anonymous
  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
- November 29, 2011 at 9:08 pm #6350
  Anonymous
  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?
- December 1, 2011 at 8:00 pm #6354
  Anonymous
  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
  -in:file:fullatom
  -out:overwrite true
  -out:file:fullatom
  -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:extended
  -loops:build_initial
  -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,
  -Jerry
- December 2, 2011 at 7:44 pm #6357
  Anonymous
  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
  http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_comparative_modeling.html
  
  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
- December 2, 2011 at 2:39 am #6356
  Anonymous
  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…..?)
- December 3, 2011 at 1:24 am #6358
  Anonymous
  Maybe this will help with the grishin format?
  
  http://www.rosettacommons.org/node/1859
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