Octopus uses machine learning techniques to figure out where in a large protein the transmembrane helicies are. Octopus isn’t required to use RosettaMP, it’s just useful to help find the transmembrane domain if you don’t already know it. (Rosetta doesn’t use the Octopus output itself, it uses the span file. Octopus is just used as a convenient way of generating the span file, but it’s not needed. You can write a span file directly.)
But you do know where your transmembrane helix is. So instead of running your protein through Octopus, you can manually edit a span file to define the residues which correspond to your transmembrane helix. So long as you know where in your protein your transmembrane residues are, you should be able to specify them in the span file.
.
