so far, I have successfully applied fold&dock to built symmetric homotetramers of the transmembrane helix of a single-anchored membrane protein. However, now I would like to model a hetero(di/tri)meric complex with each subunit being a single transmembrane a-helix. If at least one of the helices had a different membrane topology, I could simply fuse them into a single polypeptide chain, which Rosetta could fold. The problem is that all helices have the same membrane topology. I tried to introduce a transmembrane helix of opposite topology to connect the other two helices. This linker helix would of course interact with the other helices, too, so I wanted to keep this helix at a distance by using constraints. Unfortunately, distance constraints do not work with the membrane abinitio protocol. I modified the protocol according to https://www.rosettacommons.org/content/membrane-ab-initio-modeling-appli..., but it didn't work for me.
Is there any way I can built these heteromultimers with Rosetta's abinitio approach? Or can - alternatively - the same degree of flexibility of the helical structure in the abinitio protocol be achieved by a docking approach?
Thanks a lot for your help!