I'm quite new to Rosetta and I current got a problem when try to modelling a two-domain transmembrane protein.
The protein has two transmembrane domain (chain A, start from residue 1 and chain B, also start from residue 1). There is no covalent linking between the two domains.
The template I used is a crystal structure of another protein from same family, which also has two domains and got ~60% sequence similarity. The main different is the protein been modelled has some long loops between transmembrane helix whereas the template don’t have.
As the template contains the information of surface interactions between domains, I think I should model them together. I’m following the tutorial in https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial
However, which does not contain information on how make Rosetta read span and frag files for different domain.
Thanks a lot in advance!!