How to use the parmed.gromacs.GromacsTopologyFile function in ParmEd

def test_atomtyping(self, mol_name):
        top_filename = '{}.top'.format(mol_name)
        gro_filename = '{}.gro'.format(mol_name)
        top_path = os.path.join(self.resource_dir, top_filename)
        gro_path = os.path.join(self.resource_dir, gro_filename)

        structure = pmd.gromacs.GromacsTopologyFile(top_path, xyz=gro_path,
                                                    parametrize=False)
        known_opls_types = [atom.type for atom in structure.atoms]

        print("Typing {}...".format(mol_name))
        typed_structure = OPLSAA.apply(structure)

        generated_opls_types = list()
        for i, atom in enumerate(typed_structure.atoms):
            message = ('Found multiple or no OPLS types for atom {} in {} ({}): {}\n'
                       'Should be atomtype: {}'.format(
                i, mol_name, top_filename, atom.type, known_opls_types[i]))
            assert atom.type, message
            generated_opls_types.append(atom.type)

        both = zip(generated_opls_types, known_opls_types)

def by_name(cls, basename, parameterized=False):

        mol2_path, top_path, gro_path = cls.available()[basename]
        if parameterized:
            # structure = pmd.gromacs.GromacsTopologyFile(top_path, xyz=gro_path,
            #                                         parametrize=parameterized)
            structure = pmd.gromacs.GromacsTopologyFile(top_path, xyz=gro_path,
                                                    parametrize=False)
            structure.title = structure.title.replace(' GAS', '')
        else:
            # structure = pmd.gromacs.GromacsTopologyFile(pdb_path, xyz=pdb_path,
            #                                         parametrize=False)
            structure = pmd.load_file(mol2_path, structure=True)
            structure.title = structure.title.replace(' GAS', '')

        return structure

#Import ParmEd
    import parmed
    #Require version 2.0.4 or later of ParmEd, otherwise ParmEd corrupts [ defaults ] section in GROMACS topologies with incorrect FudgeLJ/FudgeQQ
    try:
        ver = parmed.version
    except:
        oldParmEd = Exception('ERROR: ParmEd is too old, please upgrade to 2.0.4 or later')
        raise oldParmEd
    if ver < (2,0,4):
        raise RuntimeError("ParmEd is too old, please upgrade to 2.0.4 or later")


    #Read AMBER to ParmEd object
    structure = parmed.amber.AmberParm( in_prmtop, in_crd )
    #Make GROMACS topology
    gromacs_topology = parmed.gromacs.GromacsTopologyFile.from_structure( structure )
    #Write
    parmed.gromacs.GromacsTopologyFile.write( gromacs_topology, out_top )
    if precision == None:
        parmed.gromacs.GromacsGroFile.write( gromacs_topology, out_gro )
    else:
        parmed.gromacs.GromacsGroFile.write( gromacs_topology, out_gro, precision = precision )

    return out_top, out_gro

#Require version 2.0.4 or later of ParmEd, otherwise ParmEd corrupts [ defaults ] section in GROMACS topologies with incorrect FudgeLJ/FudgeQQ
    try:
        ver = parmed.version
    except:
        oldParmEd = Exception('ERROR: ParmEd is too old, please upgrade to 2.0.4 or later')
        raise oldParmEd
    if ver < (2,0,4):
        raise RuntimeError("ParmEd is too old, please upgrade to 2.0.4 or later")


    #Read AMBER to ParmEd object
    structure = parmed.amber.AmberParm( in_prmtop, in_crd )
    #Make GROMACS topology
    gromacs_topology = parmed.gromacs.GromacsTopologyFile.from_structure( structure )
    #Write
    parmed.gromacs.GromacsTopologyFile.write( gromacs_topology, out_top )
    if precision == None:
        parmed.gromacs.GromacsGroFile.write( gromacs_topology, out_gro )
    else:
        parmed.gromacs.GromacsGroFile.write( gromacs_topology, out_gro, precision = precision )

    return out_top, out_gro

Merging should work fine on general topology files. However, if molecule_names and/or molecule_numbers are provided the input topologies must contain single-molecule, single-residue topologies. Molecule_numbers are used to replicate the input topologies via ParmEd, and molecule_names are used to change the residue names from the input topologies.
    """

    #PRELIMINARIES
    N_tops = len( input_topologies )

    #Check for obvious input problems - do we have the right number of everything, do all the input files exist
    if molecule_numbers != None:
        assert len( molecule_numbers ) == N_tops, "Must provide same number of molecule numbers as topology files."
    for filenm in input_topologies:
        assert( os.path.isfile( filenm )), "Error: Can't find input file %s provided to merge_topologies." % filenm

    #WORK ON TOPOLOGIES
    tops = []
    for filenm in input_topologies:
        top = parmed.gromacs.GromacsTopologyFile( filenm )
        tops.append( top )

    #List numbers of each molecule if not provided
    if molecule_numbers == None:
        molecule_numbers = [ 1] * N_tops

    #Check that we've been provided with the correct number of molecule_names if any
    if molecule_names != None:
        total_molecules = 0
        for topnr in range(N_tops):
            total_molecules += len( tops[topnr].residues )
        assert total_molecules == len( molecule_names ), "Must provide a number of molecule names equal to your total number of residues, but you have %s and %s, respectively." % ( len( molecule_names), total_molecules )

        #Rename residues
        ctr = 0
        for topnr in range(N_tops):