I am trying to model the C-terminal tail for a membrane protein which is not resolved in the crystal structure and run MD afterwards. It's 40 residues long, but disordered. I am choosing FloppyTail protocol. Since the protein is sitting in a membrane, Z component of all residues' coordinates should be more than a specific value, such that tail be out of the membrane and fall into the cytoplasmic region completely.
What I am doing so far is to do the sampling starting with the protein attached to a tail which is extended into space, without any constraint, and then choose those predicted models that have a proper Z values for the tail - which clearly wastes computational time. I also thought of having the membrane as well in my PDB input and then model the tail, maybe I should try that.
It looks more reasonable though to use some constraints. I'm just not sure which constrain type I should choose to constrain Z of all tail residues to be more than let's say 12. I would appreciate any suggestion you might have on which type of constraint I shall choose in this case.
I will attach the options I have used for FloppyTail as well. I'd also appreciate any comments on them.