change_atom_name

cation = mb.load('cation.mol2')

for idx, particle in enumerate(cation.particles()):
    if idx == 0:
        particle.name = 'C_E'
        
# Atom type system
# `structure` is a parmed structure
# Have to change the name or parmed will error when trying to save the structure
for atom in structure.atoms:
    if atom.name == 'C_E':
        atom.name = 'CE'