external_bonds = [external_bonds[0], external_bonds[-1]] + external_bonds[1:-1] if len(external_bonds) > 2 and len(external_bonds[-1].name) <= 2 else external_bonds # Hack to get rid of atom ordering diffs

def check_glycam_conversion():
    """
    Takes leaprc and lib files and uses parmed to write out a ffxml. 
    
    Simplified from openmmtools/amber/convert_amber.py's `convert_leaprc()`
    
    Note that the output of this function is not the final GLYCAM_06j-1.xml in openmmforcefields/amber/ffxml nor 
    openmm/app/data/amber14/. Additional post processing steps are necessary to obtain the final ffxml version. 
    See `modify_glycan_ffxml()` in openmmforcefields/amber/convert_amber.py.
    
    """
    import os 
    import parmed
    from io import StringIO
    import re
    
    _loadoffre = re.compile(r'loadOff (\S*)', re.I)
    _sourcere = re.compile(r'source (\S*)', re.I)
    ignore = {'solvents.lib', 'atomic_ions.lib', 'ions94.lib', 'ions91.lib',
              'phosphoaa10.lib'}
    
    input_file = "glycam/leaprc.GLYCAM_06j-1"
    output_file = "glycam/GLYCAM_06j-1.xml"
    
    # Pre-process leaprc before converting
    with open(input_file, 'rt') as f:
        lines = [ line if '#' not in line else line[:line.index('#')] for line in f.readlines() ]
    new_lines = []
    for line in lines:
        if (ignore is not None and _loadoffre.findall(line) and
        _loadoffre.findall(line)[0] in ignore):
            continue
        new_lines += line
    leaprc = StringIO(''.join(new_lines))
    
    # Convert leaprc into ffxml
    override_level = 1 
    params = parmed.amber.AmberParameterSet.from_leaprc(leaprc)
    params = parmed.openmm.OpenMMParameterSet.from_parameterset(params, remediate_residues=(False))
    if override_level:
        for name, residue in params.residues.items():
            residue.override_level = override_level
    
    params.write(output_file, provenance=None, write_unused=True, improper_dihedrals_ordering='amber', skip_duplicates=False, is_glycam=True)