old_contents: #!/bin/env python
  
  """
  Illustrate how to combine a SMIRNOFF parameterized small molecule with an AMBER parameterized protein using ParmEd.
  
  """
  
  #
  # Load and parameterize the small molecule
  #
  
  # Load the small molecule
  from openforcefield.utils import get_data_filename
  ligand_filename = get_data_filename('molecules/toluene.mol2')
  molecule = Molecule.from_file(ligand_filename)
  
  # Load the smirnoff99Frosst force field
  from openforcefield.typing.engines import smirnoff
  forcefield = smirnoff.ForceField('smirnoff99Frosst.offxml')
  
  # Create a ParmEd structure for the molecule
  molecule_structure = forcefield.create_parmed_structure(topology=molecule.to_topology(), positions=molecule.positions)
  print('Molecule:', molecule_structure)
  
  #
  # Load and parameterize the protein
  #
  
  # Load the protein topology
  from openforcefield.utils import generate_protein_structure
  protein_pdb_filename = get_data_filename('proteins/T4-protein.pdb')
  protein_pdbfile = app.PDBFile(protein_pdb_filename)
  
  # Load the AMBER protein force field, along with a solvent force field
  from simtk.openmm import app
  protein_forcefield = 'amber99sbildn.xml'
  solvent_forcefield = 'tip3p.xml'
  forcefield = app.ForceField(protein_forcefield, solvent_forcefield)
  
  # Parameterize the protein
  protein_system = forcefield.createSystem(proteinpdb.topology)
  
  # Create a ParmEd Structure for the protein
  protein_structure = parmed.openmm.load_topology(proteinpdb.topology,
                                                  protein_system,
                                                  xyz=proteinpdb.positions)
  print('Protein:', protein_structure)
  
  # Combine the ParmEd Structure objects to produce a fully parameterized complex
  # that can now be exported to AMBER, CHARMM, OpenMM, and other packages
  # Note that the addition should always add the small molecule second so the box vectors if the first item (the protein) are to be preserved
  complex_structure = protein_structure + molecule_structure
  print('Complex:', complex_structure)
  
  # TODO: How can we add solvent while ensuring the ligand doesn't overlap with solvent molecules?
  # TODO: Can we have SMIRNOFF ForceField create an OpenMM ffxml file for the ligand, and then use the OpenMM pipeline?
  # TODO: Or can OpenMM just use dummy parameters?
  
new_contents: #!/bin/env python
  
  """
  Illustrate how to combine a SMIRNOFF parameterized small molecule with an AMBER parameterized protein using ParmEd.
  
  """
  
  #
  # Load and parameterize the small molecule
  #
  
  # Load the small molecule
  from openforcefield.utils import get_data_filename
  ligand_filename = get_data_filename('molecules/toluene.mol2')
  molecule = Molecule.from_file(ligand_filename)
  
  # Load the smirnoff99Frosst force field
  from openforcefield.typing.engines import smirnoff
  forcefield = smirnoff.ForceField('smirnoff99Frosst.offxml')
  
  # Create a ParmEd structure for the molecule
  molecule_structure = forcefield.create_parmed_structure(topology=molecule.to_topology(), positions=molecule.positions)
  print('Molecule:', molecule_structure)
  
  #
  # Load and parameterize the protein
  #
  
  # Load the protein topology
  protein_pdb_filename = get_data_filename('proteins/T4-protein.pdb')
  protein_pdbfile = app.PDBFile(protein_pdb_filename)
  
  # Load the AMBER protein force field, along with a solvent force field
  from simtk.openmm import app
  protein_forcefield = 'amber99sbildn.xml'
  solvent_forcefield = 'tip3p.xml'
  forcefield = app.ForceField(protein_forcefield, solvent_forcefield)
  
  # Parameterize the protein
  protein_system = forcefield.createSystem(proteinpdb.topology)
  
  # Create a ParmEd Structure for the protein
  protein_structure = parmed.openmm.load_topology(proteinpdb.topology,
                                                  protein_system,
                                                  xyz=proteinpdb.positions)
  print('Protein:', protein_structure)
  
  # Combine the ParmEd Structure objects to produce a fully parameterized complex
  # that can now be exported to AMBER, CHARMM, OpenMM, and other packages
  # Note that the addition should always add the small molecule second so the box vectors if the first item (the protein) are to be preserved
  complex_structure = protein_structure + molecule_structure
  print('Complex:', complex_structure)
  
  # TODO: How can we add solvent while ensuring the ligand doesn't overlap with solvent molecules?
  # TODO: Can we have SMIRNOFF ForceField create an OpenMM ffxml file for the ligand, and then use the OpenMM pipeline?
  # TODO: Or can OpenMM just use dummy parameters?
  
subject: Remove unused import