Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Error encountered during Rosetta loop modeling
- This topic has 3 replies, 3 voices, and was last updated 9 years, 9 months ago by
Anonymous.
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November 25, 2014 at 10:17 am #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: 184The 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: 184To better understand the situation, inside the folder “prova” are present both pdb and loop files.
How can I solve this problem?
Best regards,
Max
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November 25, 2014 at 3:41 pm #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.
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November 27, 2014 at 10:56 am #10651
Anonymous
Thanks everyone!
Max
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November 26, 2014 at 3:37 pm #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”).
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