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

[Anonymous]

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!

[Anonymous]

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

[Anonymous]

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 I guess this was just a case of outdated documentation, so no worries.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.

 

[Author]

Posts