I am trying to model missing residues from a solved structure of a membrane protein to prepare it for MD simulations. Some of these residues (~10) are follow a transmembrane segment at the C-terminus of the protein. After loop refinement, these residues always end up in the "membrane region" that I know from the solved TMs in the structure.
However, I know these loop residues are soluble and should not be in this region. I would like to specify some sort of planar spatial restraint to describe where the residues can be, e.g. residues allowed above 10 A in the z direction? Is there a way to specify this?