Error encountered during Rosetta loop modeling

[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

[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.

[Anonymous]

Thanks everyone!

Max

[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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