# RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?

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RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?
#1

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!

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Thu, 2020-05-14 11:15
brspurri

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

Thu, 2020-05-14 12:10