I am trying to run a basic antibody/antigen design/dock simulaton using RosettaAntibodyDesign (from Rosetta 3.12)
I am using the command:
antibody_designer.macosclangrelease \ -database /path/to/database/ \ -do_dock \ -use_epitope_constraints \ -nstruct 5 -in:file:s complex_renumbered.pdb \ -seq_design_cdrs H1 H2 H3 \ -primary_cdrs H3 \ -mintype relax \ -run_snugdock \ -run_relax \ -out:path:all ./output
And it appears to run well - it outputs the predicted designed structures. However, as part of the output, I am seeing:
[ WARNING ] The following options have been set, but have not yet been used: -antibody:design:run_relax -antibody:run_snugdock
which indicates the relaxing and snugdock tasks did not run.
How can I get RosettaAntibodyDesign to respect these flags and tasks? According to the documentation, it looks like I am specifying the flags correctly.