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RosettaCommons / rosetta

The Rosetta Bio-macromolecule modeling package.
https://www.rosettacommons.org
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Errors when run docking_protocol.linuxgccrelease #96

Closed Luckken21 closed 1 week ago

Luckken21 commented 2 months ago

[ERROR] Exception caught by JobDistributor for job test1_A_local_dock_0001

[ ERROR ]: Caught exception:

File: src/core/conformation/Conformation.hh:514 [ ERROR ] UtilityExitException ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose. I meet the problem when using ~/Rosseta/rosetta.source.release-371/main/source/bin/docking_protocol.linuxgccrelease -in:file:s input_files/test1_A.pdb -in:file:native input_files/test_A.pdb -nstruct 1 -partners A_B -dock_pert 3 8 -ex1 -ex2aro -out:path:all output_files -out:suffix _local_dock Thanks a lot if you can help me

roccomoretti commented 2 months ago

The -partners A_B specifies you want to dock chain B against chain A. Does your input file (input_files/test1_A.pdb) contain both chain A and chain B? Both chains need to be present in the input file, but don't (necessarily) need to be in the correct relative orientation.

roccomoretti commented 1 week ago

Marking this as "closed", as I hope your issue has been addressed. If that assessment is incorrect, feel free to re-open or open up a new issue with more details.