Docking

Hello world, 

How can I dock one protein into interface between two proteins? I am new to rosetta software and I am still leraning. I study a protein that bridges two other proteins togeter and I was wondering how can I model that? I would apreciate your input in directing me to the tutorials or documentation. 

Thanks. Cheems

Hello Rosetta people,

I performed a protein protein docking of a protain A + ligand A (74 atoms) noted as binary_complex to protein B, and got warning of missing atoms, still could get docked P-P poses, however, the ligand is not intact, some atoms missed in the output binary_complex. I also added the -ignore_unrecognized_res flag in the command.

I am currently working on a simple test with antibodies.

I have a question in this regard, can I use deepab instead of rosetta antibody to create antibody structures? When I looked at the snugdock paper, it seems that there is an additional protocol when using a tool other than rosetta antibody, but I know that deepab creates structures based on rosetta. So I am wondering if I can proceed in the same way as rosetta antibody when using deepab. 

I've done some ligand docking using cognate ligands, so used the starting coordinates of the input sdf file.  I now want to dock some analogues and want to use the same starting coordinates.  Is there a way to find what coordinates were used for the initial docking?

Thanks