OpenMM does not give progress for minimization, just wait...
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (ATOM      1 HO5'   A A   1       0.246  -1.951   0.293  1.00  0.00           H  , ATOM      1 HO5'   A A   1       0.246  -1.951   0.293  1.00  0.00           H  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
example1 (2).pdb ...
Traceback (most recent call last):
  File "/home/ubuntu/rna-tools/rna_tools/tools/md/rna_minimize.py", line 54, in <module>
    modeller.addHydrogens(forcefield)
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/modeller.py", line 946, in addHydrogens
    system = forcefield.createSystem(newTopology, rigidWater=False, nonbondedMethod=CutoffNonPeriodic)
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/forcefield.py", line 1206, in createSystem
    templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/forcefield.py", line 1420, in _matchAllResiduesToTemplates
    raise ValueError('No template found for residue %d (%s).  %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
ValueError: No template found for residue 1 (A).  The set of atoms matches AN, but the bonds are different.  Perhaps the chain is missing a terminal group?
DONE!