I’m going to hazard a guess that you have a centroid protein structure, which doesn’t have HA atoms present. Is it in centroid or fullatom?
The types are in rosetta_database/chemical/residue_type_sets/ centroid or fa_standard, depending on if you have centroids or all atoms. I think CS-rosetta is using centroids (at least for the early stages).
I see a patch protein_centroid_with_HA.txt, which looks like it should allow the creation of centroid residues which also have HA atoms. It’s active by default, but that doesn’t mean the code knows to add HAs. If centroid-ness turns out to be the problem, let me know what your command lines are and I’ll see if I can find where the pose is created to tell it to use centroid-with-HA (no promises that I can do it or that it will work).
You can also just fiddle with the distances and use only backbone hydrogens in your constraints.