Error encountered during Rosetta loop modeling

Member Site Forums Rosetta 3 Rosetta 3 – Applications Error encountered during Rosetta loop modeling

Viewing 2 reply threads
  • Author
    Posts
    • #2079
      Anonymous

        Hi everyone,

        I’m trying to run Rosetta kinematic loop on my computer but I got an error message after few seconds:

        ERROR: Cannot open PDB file “input_pdb”
        ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 184

        The comand that I have used and the screenshot of the error page is shown below:

        [massimiliano@luisi10 prova]$ /rosetta3.4/rosetta_source/bin/loopmodel.linuxgccrelease -database /rosetta3.4/rosetta_database/ -loops:remodel perturb_kic -in:file:native 4k1c.pdb -in:file:fullatom -loops:loop_file 4k1c.loop -nstruct 100 -ex1 -ex2 -overwrite

        core.init: Mini-Rosetta version esportato from unknown
        core.init: command: /home/massimiliano/Desktop/rosetta3.4/rosetta_source/bin/loopmodel.linuxgccrelease -database /home/massimiliano/Desktop/rosetta3.4/rosetta_database/ -loops:remodel perturb_kic -in:file:native 4k1c.pdb -in:file:fullatom -loops:loop_file 4k1c.loop -nstruct 100 -ex1 -ex2 -overwrite
        core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1480154873 seed_offset=0 real_seed=1480154873
        core.init.random: RandomGenerator:init: Normal mode, seed=1480154873 RG_type=mt19937
        protocols.loop_build.LoopBuild: ==== Loop protocol: =================================================
        protocols.loop_build.LoopBuild: remodel perturb_kic
        protocols.loop_build.LoopBuild: intermedrelax no
        protocols.loop_build.LoopBuild: refine no
        protocols.loop_build.LoopBuild: relax no
        core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6225 residue types
        core.import_pose.import_pose: PDB File:input_pdb not found!

        ERROR: Cannot open PDB file “input_pdb”
        ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 184

        To better understand the situation, inside the folder “prova” are present both pdb and loop files.

        How can I solve this problem?

        Best regards,

        Max

      • #10639
        Anonymous

          in:file:native is only used for comparison to the output pdb, and other protocol-specific places. You want to pass the option in:file:s for the PDB you will be modeling.

        • #10651
          Anonymous

            Thanks everyone!

            Max

          • #10645
            Anonymous

              In Rosetta3.4 and before, the loopmodel application actually wants its input specified with the flag “-loops:input_pdb”.

              In Rosetta3.5 and after, the loopmodel application uses the standard “JD2” input options. (So specifying the input pdb with “-in:file:s”).

          Viewing 2 reply threads
          • You must be logged in to reply to this topic.