When ParmEd tries to apply a patch to a residue, it checks to see if the net charge of the patched residue is integral:

This is incompatible with the CHARMM36 nucleic acid force field, as I found when trying to convert it to OpenMM FFXML format. Specifically, applying terminal patches to the residues at the ends of a chain of nucleic acids can yield patched residues with non-integral net charges, even though the final chain will have an integral net charge.

I hacked around this for our conversion by removing the check, but it's not clear if that's a good idea in general, so maybe an option to disable it if desired would be better?