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:
[ ERROR ] UtilityExitException
ERROR: Must define ensemble file for both partners
My full flags are as follow:
-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!