I'd like to fold-and-dock a trimeric transmembrane domain. I mostly have the "Fold And Dock" working following the example in demos/public/symmetry_examples/fold-and-dock/. However this is treating the transmembrane helixes as though they are in solvent (so for example any hydrophilic groups always rotate outwards). I'd like to do something which is a combination of "Membrane Abinitio" and "Fold and Dock". Is this possible, and how do I do it?
Can I run membrane_abinitio2.linuxgccrelease app with symmetry options like -symmetry:symmetry_definition etc?
Or, can I pass membrane options like -abinitio:membrane -in:file:lipofile -membrane:Menv_penalties etc to the minirosetta.linuxgccrelease app where -broker:setup is pointing to "CLAIMER FoldandDockClaimer"?
I'm confused about how to combine these two protocols, or if it is even possible to combine them at all. Please let me know the best way to go about this.