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

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    • May 14, 2020 at 6:15 pm #3423
      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!

      • May 14, 2020 at 7:10 pm #15288
        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

          • May 14, 2020 at 7:24 pm #15289
            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 I guess this was just a case of outdated documentation, so no worries.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.

               

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