text: from perses import dualtopology
  
  ligands = []
  ligands.append("Glycine")
  ligands.append("Lysine")
  ligands.append("Alanine")
  
  dualtop = dualtopology.DualTopology(ligands)
  dualtop.createDualTopology()
  
  print("Atom indeces from each substructure:")
  print(dualtop.each_molecule_N)
  
  dualtop.savePDBandFFXML(pdb_filename="3_aminos.pdb")
  
  
  
  