Going back and forth between ParmEd and and GMSO raises issues

[CalCraven]

In order to get feature parity with Foyer, we need to test back and forth with different ParmEd structures. As such, a workflow below might be useful.

import mbuild as mb
import foyer
cpd = mb.load("CC[N+](=O)[O-]", smiles=True)
opls = foyer.Forcefield(name="oplsaa")
pmd = cpd.to_parmed()

from gmso.external import from_parmed, to_parmed
top = from_parmed(pmd, refer_type=False)
pmd = to_parmed(top)

typed_pmd = opls.apply(pmd, assert_improper_params=False)

However, this leads to the output

AttributeError                            Traceback (most recent call last)
Input In [5], in <module>
      9 from gmso.external import from_parmed, to_parmed
     10 top = from_parmed(pmd, refer_type=False)
---> 11 pmd = to_parmed(top)
     13 typed_pmd = opls.apply(pmd, assert_improper_params=False)

File ~/Dropbox/Mac/Documents/Vanderbilt/Research/MoSDeF/gomc-gmso-paper/gmso/gmso/external/convert_parmed.py:482, in to_parmed(top, refer_type)
    477 else:
    478     atomic_number = 0
    479 pmd_atom = pmd.Atom(
    480     atomic_number=atomic_number,
    481     name=site.name,
--> 482     mass=site.mass.to(u.amu).value,
    483     charge=site.charge.to(u.elementary_charge).value,
    484 )
    485 pmd_atom.xx, pmd_atom.xy, pmd_atom.xz = site.position.to(
    486     "angstrom"
    487 ).value
    489 # Add atom to structure

AttributeError: 'NoneType' object has no attribute 'to'

To fix this, line 482 should be changed based on the elements mass.

site.element.mass.to(u.amu).value

python version 3.8
gmso version 0.8.0

[chrisjonesBSU]

This should be fixed by #737