I have been trying to use matcher to specify a single Asp/Glue bound to two metal ions, on oxygen atom to each metal atom, and I have gotten several different errors when applying the secondary matching algorithm. My approach is to use upstream secondary matching to apply an additional bond length constraint between the second metal atom and the second O atom of a D/E ligand that was already matched to the first metal atom. Attached are the test constraint file (testing only a single constraint with secondary matching applied) and the log file, which--for some reason that I cannot figure out--gives an error about H-atom definitions in GLY residues.
The pdb that I used for matching was prepared with rosetta's pdb cleaning script and has worked fine for previous matcher tests. I have previously (though not in this case) had issues with matcher not being able to locate "ALGORITHM_INFO::END" from secondary matching even when it is present in the cst.