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Noncanonical backbones are getting into some pretty heavy lifting. Rosetta can do this, but something this complicated needs hands-on developer tweaking to get it done. Release 3.2.1 can’t do it; current developer trunk can’t do it, although I think there’s a branch that can.
If the clash is in a constant region of the protein, you can (and probably should) just ignore it. You say you are modifying a loop near the ligand. If the residues that are directly attached to the GFP fluorophore are not being moved, then their clashes can’t be relaxed and thus just add a constant large score. A clash between the ligand the neighboring residues will not affect kinematic modeling of a loop that is proximal in space (so long as it’s not next to the ligand in primary sequence). Your total scores will be ugly, but they’ll be okay once you subtract off the large constant clash. Does this make sense (and does it apply to your case?)