OpenMM does not give progress for minimization, just wait...
tetraloop_mdr.pdb ...
Traceback (most recent call last):
  File "/home/ubuntu/rna-tools/rna_tools/tools/md/rna_minimize.py", line 42, in <module>
    pdb = PDBFile(f)
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/openmm/app/pdbfile.py", line 163, in __init__
    self.positions = self._positions[0]
IndexError: list index out of range
DONE!