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.
On 2/22/17 2:28 PM, Shyam Saladi wrote: > 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?
Sure, that's straightforward. See https://salilab.org/modeller/9.18/manual/node28.html for adding additional restraints to the modeling and https://salilab.org/modeller/9.18/manual/node108.html for the restraints themselves. You probably want something like a harmonic lower bound on the z coordinate, e.g.
rsr.add(forms.lower_bound(group=physical.xy_distance, feature=features.z_coordinate(at['CA:35']), mean=10.0, stdev=0.1))
(This would restrain the CA atom in residue 35.)
Ben Webb, Modeller Caretaker