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Ensemble file required for both partners with docking prepack protocol

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Ensemble file required for both partners with docking prepack protocol
#1

Hi all,

I'm currently running the docking prepack protocol before SnugDock, and the documentation page (https://www.rosettacommons.org/docs/latest/application_documentation/docking/docking-prepack-protocol) indicates you can provide an ensemble file for just one of the partners, or both partners. I have an ensemble of antibody structures + one antigen structure. However, when I try providing an ensemble file for just the antibody, I get this error:

 

[ ERROR ]: Caught exception:


File: src/protocols/docking/DockingEnsemblePrepackProtocol.cc:155
[ ERROR ] UtilityExitException
ERROR: Must define ensemble file for both partners

 

My full flags are as follow:

-s /dartfs/rc/lab/G/Grigoryanlab/home/coy/AbAgTERMs/test_abag_files/cluspro.7wk9sphinxabAgClusProOut/model.000.00.pdb
-database /dartfs/rc/lab/G/Grigoryanlab/home/coy/Rosetta/rosetta.source.release-296/main/database
-docking:partners C_HL
-ensemble2 /dartfs/rc/lab/G/Grigoryanlab/home/coy/AbAgTERMs/test_abag_files/testEnsemblesDiffAbs.txt
-out:path:all /dartfs/rc/lab/G/Grigoryanlab/home/coy/AbAgTERMs/test_abag_files/prepack_test_ens # like models_path_out/

 

And my ensemble file simply contains paths to two antibody structures, with the same residues / chains / etc. for the antibodies as in the model.000.00.pdb

 

Is the documentation just not up to date / there a reason why I do need to provide ensemble files for both partners, or am I doing something wrong / interpreting this error incorrectly? Many thanks!

- Coy

 

Category: 
Post Situation: 
Tue, 2022-03-29 14:26
katherinemccoy