new_contents: """
  Generate PDB file containing periodic box data.
  
  """
  
  from simtk import openmm, unit
  from simtk.openmm import app
  
  prmtop_filename = 'alanine-dipeptide.prmtop'
  crd_filename = 'alanine-dipeptide.crd'
  pdb_filename = 'alanine-dipeptide.pdb'
  
  # Read topology and positions.
  prmtop = app.AmberPrmtopFile(prmtop_filename)
  inpcrd = app.AmberInpcrdFile(crd_filename)
  
  # Write PDB.
  outfile = open(pdb_filename, 'w')
  app.PDBFile.writeFile(prmtop.topology, inpcrd.positions, file=outfile, keepIds=True)
  outfile.close()
  
  
subject: Add script to generate proper alanine-dipeptide explicit solvent PDB file with CRYST record.