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 (HETATM    3  C   UNK     0      16.330  14.504  57.819  0.00  0.00           C  , HETATM    2  C   UNK     0      15.027  14.682  57.030  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM    4  C   UNK     0      15.878  13.477  58.828  0.00  0.00           C  , HETATM    3  C   UNK     0      16.330  14.504  57.819  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM    5  C   UNK     0      15.112  12.525  57.903  0.00  0.00           C  , HETATM    4  C   UNK     0      15.878  13.477  58.828  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM    7  C   UNK     0      15.452  12.902  55.561  0.00  0.00           C  , HETATM    5  C   UNK     0      15.112  12.525  57.903  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM    8  C   UNK     0      15.142  13.773  54.369  0.00  0.00           C  , HETATM    7  C   UNK     0      15.452  12.902  55.561  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM    9  C   UNK     0      17.695   8.699  50.732  0.00  0.00           C  , HETATM    8  C   UNK     0      15.142  13.773  54.369  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   10  C   UNK     0      17.180   9.883  51.464  0.00  0.00           C  , HETATM    9  C   UNK     0      17.695   8.699  50.732  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   11  N   UNK     0      16.407   9.785  52.569  0.00  0.00           N  , HETATM    1  N   UNK     0      14.722  13.290  56.749  0.00  0.00           N  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   12  C   UNK     0      15.942  10.858  53.230  0.00  0.00           C  , HETATM   10  C   UNK     0      17.180   9.883  51.464  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   13  C   UNK     0      16.263  12.114  52.768  0.00  0.00           C  , HETATM   12  C   UNK     0      15.942  10.858  53.230  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   14  C   UNK     0      15.960  13.399  53.201  0.00  0.00           C  , HETATM   13  C   UNK     0      16.263  12.114  52.768  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   15  C   UNK     0      16.569  14.287  52.330  0.00  0.00           C  , HETATM   14  C   UNK     0      15.960  13.399  53.201  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   16  N   UNK     0      17.209  13.562  51.417  0.00  0.00           N  , HETATM   11  N   UNK     0      16.407   9.785  52.569  0.00  0.00           N  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   17  C   UNK     0      17.041  12.238  51.657  0.00  0.00           C  , HETATM   15  C   UNK     0      16.569  14.287  52.330  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   18  N   UNK     0      17.479  11.119  51.034  0.00  0.00           N  , HETATM   16  N   UNK     0      17.209  13.562  51.417  0.00  0.00           N  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   19  H   UNK     0      17.776  13.892  50.606  0.00  0.00           H  , HETATM    6  H   UNK     0      13.686  13.149  56.599  0.00  0.00           H  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   21  C   UNK     0      15.436  13.930  61.071  0.00  0.00           C  , HETATM   17  C   UNK     0      17.041  12.238  51.657  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   22  C   UNK     0      15.077  12.617  61.688  0.00  0.00           C  , HETATM   21  C   UNK     0      15.436  13.930  61.071  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   23  C   UNK     0      16.188  12.012  62.502  0.00  0.00           C  , HETATM   22  C   UNK     0      15.077  12.617  61.688  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   24  N   UNK     0      16.835  13.049  63.277  0.00  0.00           N  , HETATM   18  N   UNK     0      17.479  11.119  51.034  0.00  0.00           N  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   25  C   UNK     0      17.497  14.097  62.538  0.00  0.00           C  , HETATM   23  C   UNK     0      16.188  12.012  62.502  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   26  C   UNK     0      16.890  14.245  61.200  0.00  0.00           C  , HETATM   25  C   UNK     0      17.497  14.097  62.538  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   27  C   UNK     0      16.831  13.059  64.715  0.00  0.00           C  , HETATM   26  C   UNK     0      16.890  14.245  61.200  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   28  N   UNK     0      15.821  12.609  65.498  0.00  0.00           N  , HETATM   24  N   UNK     0      16.835  13.049  63.277  0.00  0.00           N  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   29  C   UNK     0      16.143  12.760  66.804  0.00  0.00           C  , HETATM   27  C   UNK     0      16.831  13.059  64.715  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   30  N   UNK     0      15.479  12.467  67.950  0.00  0.00           N  , HETATM   28  N   UNK     0      15.821  12.609  65.498  0.00  0.00           N  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   31  C   UNK     0      16.014  12.713  69.156  0.00  0.00           C  , HETATM   29  C   UNK     0      16.143  12.760  66.804  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   32  C   UNK     0      17.266  13.276  69.249  0.00  0.00           C  , HETATM   31  C   UNK     0      16.014  12.713  69.156  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   33  C   UNK     0      17.941  13.574  68.084  0.00  0.00           C  , HETATM   32  C   UNK     0      17.266  13.276  69.249  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   34  C   UNK     0      17.396  13.323  66.835  0.00  0.00           C  , HETATM   33  C   UNK     0      17.941  13.574  68.084  0.00  0.00           C  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   35  N   UNK     0      17.777  13.488  65.559  0.00  0.00           N  , HETATM   30  N   UNK     0      15.479  12.467  67.950  0.00  0.00           N  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/internal/pdbstructure.py:537: UserWarning: WARNING: duplicate atom (HETATM   36  H   UNK     0      18.699  13.901  65.293  0.00  0.00           H  , HETATM   19  H   UNK     0      17.776  13.892  50.606  0.00  0.00           H  )
  warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
2gdi_cmp12_docked.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 (UNK).  This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field.
DONE!