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.
Thanks!
Category:
Post Situation:
Hello!
I definitely need to update the documentation. I refactored all of it a while ago, and took these options out. I will add them to the deprecated options.
Snugdock took way too long. A colleague has a Pull Request up that shortens the run time for Snugdock by a huge margin - so be on the lookout for that.
All my designs I've created and run a post relax on failed. My guess is because relax adds a lot of noise. So I removed it. You are welcome to use RAbD in a RosettaScript and relax and/or run Snugdock afterwards by calling the mover.
-Jared
Great! Thank you for the comments. I guess this was just a case of outdated documentation, so no worries.
The remaining protocol is seemingly working as expected.