Calling SnugDock from PyRosetta

Thank you so much for all of the pointers. The reason I wanted to use PyRosetta is because I run Windows OS and don’t have enough memory to run at the size of Rosetta on VM. I now have PyRosetta set up and working, but still need help calling SnugDock. I have read and understand the tutorial from the Nature Protocols paper, but that was for Rosetta. Generally I understand there are the following steps that need to be used in order to run a SnugDock run but would appreciate feedback on the methods I could use since I cannot find any SnugDock-specific code on Github as an example.  

1.) Imports

pyrosetta.rosetta

pyrosetta.rosetta.protocols.antibody

pyrosetta.rosetta.protocols.antibody.design

pyrosetta.rosetta.protocols.antibody.snugdock

2.) Load and clean the Ab and antigen structures with cleanATOM

3.) If I have only the antibody sequence and not a crystal structure, I would need to generate homology models first. I am assuming that I can skip this step and move on directly to relaxing my antibody structures to generate the ensemble list of Abs if I already have a crystal structure of my Ab. 

To determine the homology models, I was thinking of using CDR grafting in RosettaAntibodyDesign and mostly following the tutorials in the PyRosetta notebooks – or is there an easier way to do this?

1.) I would begin with a manually “docked” complex from a prelimary ZDOCK/GRAMM-X run and remove the antigen chain in the pdb file.

2.) Renumber this new Ab only file with PyIgClassify.

3.) Sequence design for the heavy chains, L1, and L3 for the pose of the Ab only .pdb file from PyIgClassify.

4.) Graft design the CDRs and sequence design L1 and L3.

5.) Model H3. I’m not sure how I can do this in PyRosetta so any guidance would be greatly appreciated. 

At this point, would the designed and grafted heavy chains, L1, and L3 along with the modeled H3 all be compiled into the same list? That is, how would I make the ensemble list of the antibody to prepack and then feed into SnugDock?

4.) Relax the antigen structure to generate the antigen ensemble list. If I already have the crystal strucure of my antibody can I jump straight into this step, avoiding making homology models and creating my antibody ensemble list from that?

Apply FastRelax to .pdb antigen and .pdb antibody. I’m assuming that if I have an ensemble list of homology models I can skip relaxing the homology antibodies.

5.) Assemble a putative docked complex with the Ab (L, H) and the antigen chain (A) by aligning to a preliminary ZDOCK/GRAMM-X/etc. run as a starting docking position. I’m assuming I would only need to do this for one of the members of the antibody ensemble list with one of the members of the antigen ensemble list for a total of 1 manually “docked” complexes as a starting point. I am aware that the order of each member of the Ab ensemble list is very important and must be L, H.

6.) Prepack the manually “docked” complex, the antibody ensemble, and the antigen ensemble. 

I am not sure if I should use prepack or set_prepack and am also not sure what my command should be for this line.

7.) Set the SnugDock flags and run.

I found this on a different forum post: 

snugdock.mpi.linuxgccrelease -s antibody_antigen_start.prepack.pdb -ensemble1 antibody_ensemble.list  -ensemble2 antigen_ensemble.list -antibody:auto_generate_kink_constraint -antibody:all_atom_mode_kink_constraint -partners LH_G –spin -dock_pert 3 8 -ex1 -ex2aro -nstruct 1000 

If I’m running this from PyRosetta on my Windows machine running Ubuntu, how would I change the command to run on my computer?

Thank you so much for all of your help!