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?
I appreciate any help in advance.