OpenMM does not give progress for minimization, just wait...
rna_ligand_complex.pdb ...
1 nm
Energy at Minima is -107165.620 kcal/mol
saved  rna_ligand_complex_min.pdb
Cmd: rna_minimize.py -sp rna_ligand_complex.pdb
Execution time: 86:16:38.570  start: 13:06:05 end: 04:22:43  
DONE!