Sage has no bonded parameters for diatomic oxygen?

[timbernat]

Describe the bug
While attempting to load box full of oligomers with some small molecule gases (H2O, O2, CO2, etc.) for a packaging permeability study, I was surprised to receive an UnassignedBondError for any O2 molecules I put in. I found that a Topology containing just a single O2 molecule was enough to trigger the Exception.

To Reproduce

from openff.toolkit import Molecule, ForceField

o2 = Molecule.from_smiles('O=O')
o2.generate_conformers(n_conformers=1)
o2.assign_partial_charges(partial_charge_method='AM1BCC')

ff = ForceField('openff-2.0.0.offxml')
inc = ff.create_interchange(o2.to_topology(), charge_from_molecules=[o2])

Output

---------------------------------------------------------------------------
UnassignedBondError                       Traceback (most recent call last)
Cell In[27], line 9
      6 o2.assign_partial_charges(partial_charge_method='AM1BCC')
      8 ff = ForceField('openff-2.0.0.offxml')
----> 9 inc = ff.create_interchange(o2.to_topology(), charge_from_molecules=[o2])

File /projects/tibe3324/software/anaconda/envs/nrel-polymers/lib/python3.11/site-packages/openff/utilities/utilities.py:79, in requires_package..inner_decorator..wrapper(*args, **kwargs)
     76 except Exception as e:
     77     raise e
---> 79 return function(*args, **kwargs)

File /projects/tibe3324/software/anaconda/envs/nrel-polymers/lib/python3.11/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py:1235, in ForceField.create_interchange(self, topology, toolkit_registry, charge_from_molecules, partial_bond_orders_from_molecules, allow_nonintegral_charges)
   1232     used_registry = GLOBAL_TOOLKIT_REGISTRY
   1234 with toolkit_registry_manager(used_registry):
-> 1235     return Interchange.from_smirnoff(
   1236         force_field=self,
   1237         topology=topology,
   1238         charge_from_molecules=charge_from_molecules,
   1239         partial_bond_orders_from_molecules=partial_bond_orders_from_molecules,
   1240         allow_nonintegral_charges=allow_nonintegral_charges,
   1241     )

File /projects/tibe3324/software/anaconda/envs/nrel-polymers/lib/python3.11/site-packages/openff/interchange/components/interchange.py:161, in Interchange.from_smirnoff(cls, force_field, topology, box, positions, charge_from_molecules, partial_bond_orders_from_molecules, allow_nonintegral_charges)
    103 """
    104 Create a new object by parameterizing a topology with a SMIRNOFF force field.
    105 
   (...)    157 
    158 """
    159 from openff.interchange.smirnoff._create import _create_interchange
--> 161 return _create_interchange(
    162     force_field=force_field,
    163     topology=topology,
    164     box=box,
    165     positions=positions,
    166     molecules_with_preset_charges=charge_from_molecules,
    167     partial_bond_orders_from_molecules=partial_bond_orders_from_molecules,
    168     allow_nonintegral_charges=allow_nonintegral_charges,
    169 )

File /projects/tibe3324/software/anaconda/envs/nrel-polymers/lib/python3.11/site-packages/openff/interchange/smirnoff/_create.py:195, in _create_interchange(force_field, topology, box, positions, molecules_with_preset_charges, partial_bond_orders_from_molecules, allow_nonintegral_charges)
    190     all_assigned_constraint_indices = {tuple(key.atom_indices) for key in interchange["Constraints"].key_map}
    191     bond_like_assigned_constraint_indices = {
    192         constraint for constraint in all_assigned_constraint_indices if constraint in topological_bond_indices
    193     }
--> 195     _check_all_valence_terms_assigned(
    196         handler_class=BondHandler,
    197         topology=interchange.topology,
    198         assigned_atom_indices=assigned_bond_indices.union(bond_like_assigned_constraint_indices),
    199         valence_terms=interchange["Bonds"].valence_terms(interchange.topology),
    200     )
    202 _angles(interchange, force_field, interchange.topology)
    204 if "Angles" in force_field.registered_parameter_handlers:

File /projects/tibe3324/software/anaconda/envs/nrel-polymers/lib/python3.11/site-packages/openff/interchange/smirnoff/_base.py:108, in _check_all_valence_terms_assigned(handler_class, assigned_atom_indices, topology, valence_terms)
    105 exception.unassigned_topology_atom_tuples = unassigned_atom_tuples  # type: ignore[attr-defined]
    106 exception.handler_class = handler_class  # type: ignore[attr-defined]
--> 108 raise exception

UnassignedBondError: BondHandler was not able to find parameters for the following valence terms:

- Topology indices (0, 1): names and elements ( O), ( O), 

Computing environment (please complete the following information):

• Operating system: Rocky Linux 8.10 (Green Obsidian)
• Output of running conda list:

# Name                    Version                   Build  Channel
_openmp_mutex             4.5                  7_kmp_llvm    conda-forge
absl-py                   2.3.1              pyhd8ed1ab_0    conda-forge
aiohappyeyeballs          2.6.1              pyhd8ed1ab_0    conda-forge
aiohttp                   3.13.2          py311h0281608_0    conda-forge
aiosignal                 1.4.0              pyhd8ed1ab_0    conda-forge
ambertools                23.3            py311hda91260_3    conda-forge
amberutils                21.0                     pypi_0    pypi
annotated-types           0.7.0              pyhd8ed1ab_1    conda-forge
anyio                     4.12.0             pyhcf101f3_0    conda-forge
anytree                   2.13.0                   pypi_0    pypi
argon2-cffi               25.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      25.1.0          py311h49ec1c0_2    conda-forge
arpack                    3.8.0           nompi_h0baa96a_101    conda-forge
arrow                     1.4.0              pyhcf101f3_0    conda-forge
asttokens                 3.0.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_3    conda-forge
async-lru                 2.0.5              pyh29332c3_0    conda-forge
attrs                     25.4.0             pyhcf101f3_1    conda-forge
aws-c-auth                0.7.31               h57bd9a3_0    conda-forge
aws-c-cal                 0.7.4                hfd43aa1_1    conda-forge
aws-c-common              0.9.28               hb9d3cd8_0    conda-forge
aws-c-compression         0.2.19               h756ea98_1    conda-forge
aws-c-event-stream        0.4.3                h29ce20c_2    conda-forge
aws-c-http                0.8.10               h5e77a74_0    conda-forge
aws-c-io                  0.14.18             h2af50b2_12    conda-forge
aws-c-mqtt                0.10.7               h02abb05_0    conda-forge
aws-c-s3                  0.6.6                h834ce55_0    conda-forge
aws-c-sdkutils            0.1.19               h756ea98_3    conda-forge
aws-checksums             0.1.20               h756ea98_0    conda-forge
aws-crt-cpp               0.28.3               h3e6eb3e_6    conda-forge
aws-sdk-cpp               1.11.379            h9f1560d_11    conda-forge
babel                     2.17.0             pyhd8ed1ab_0    conda-forge
backports.zstd            1.2.0           py311h6b1f9c4_0    conda-forge
beautifulsoup4            4.14.3             pyha770c72_0    conda-forge
bleach                    6.3.0              pyhcf101f3_0    conda-forge
bleach-with-css           6.3.0                h5f6438b_0    conda-forge
blosc                     1.21.6               he440d0b_1    conda-forge
boltons                   25.0.0             pyhd8ed1ab_0    conda-forge
boost                     1.78.0          py311h92ebd52_5    conda-forge
boost-cpp                 1.78.0               h2c5509c_4    conda-forge
brotli                    1.2.0                hed03a55_1    conda-forge
brotli-bin                1.2.0                hb03c661_1    conda-forge
brotli-python             1.2.0           py311h66f275b_1    conda-forge
bson                      0.5.10             pyhd8ed1ab_0    conda-forge
bzip2                     1.0.8                hda65f42_8    conda-forge
c-ares                    1.34.6               hb03c661_0    conda-forge
c-blosc2                  2.17.1               h3122c55_0    conda-forge
ca-certificates           2025.11.12           hbd8a1cb_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                6.2.2              pyhd8ed1ab_0    conda-forge
cairo                     1.18.0               hbb29018_2    conda-forge
certifi                   2025.11.12         pyhd8ed1ab_0    conda-forge
cffi                      2.0.0           py311h03d9500_1    conda-forge
charset-normalizer        3.4.4              pyhd8ed1ab_0    conda-forge
chemspipy                 2.0.0                    pypi_0    pypi
cirpy                     1.0.2                    pypi_0    pypi
click                     8.3.1              pyh8f84b5b_1    conda-forge
click-option-group        0.5.6              pyhd8ed1ab_0    conda-forge
cloudpickle               3.1.2              pyhcf101f3_1    conda-forge
colorama                  0.4.6              pyhd8ed1ab_1    conda-forge
comm                      0.2.3              pyhe01879c_0    conda-forge
contourpy                 1.3.3           py311hdf67eae_3    conda-forge
cpython                   3.11.14         py311hd8ed1ab_2    conda-forge
cuda-nvrtc                13.1.80              hecca717_0    conda-forge
cuda-version              13.1                 h2ff5cdb_3    conda-forge
cycler                    0.12.1             pyhcf101f3_2    conda-forge
debugpy                   1.8.17          py311hc665b79_1    conda-forge
decorator                 5.2.1              pyhd8ed1ab_0    conda-forge
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deprecation               2.1.0              pyh9f0ad1d_0    conda-forge
dgl                       2.3.0           py311h1772aec_0    conda-forge
edgembar                  0.2                      pypi_0    pypi
ele                       0.2.0              pyhd8ed1ab_0    conda-forge
espaloma_charge           0.0.8              pyhd8ed1ab_3    conda-forge
exceptiongroup            1.3.1              pyhd8ed1ab_0    conda-forge
executing                 2.2.1              pyhd8ed1ab_0    conda-forge
fftw                      3.3.10          nompi_h3b011a4_111    conda-forge
filelock                  3.20.0             pyhd8ed1ab_0    conda-forge
flatbuffers               24.3.25              h59595ed_0    conda-forge
flexcache                 0.3                pyhd8ed1ab_1    conda-forge
flexparser                0.4                pyhd8ed1ab_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_3    conda-forge
fontconfig                2.15.0               h7e30c49_1    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                    hc364b38_1    conda-forge
fonttools                 4.61.0          py311h3778330_0    conda-forge
forcefield-utilities      0.5.0              pyhd8ed1ab_0    conda-forge
foyer                     1.0.0              pyhd8ed1ab_0    conda-forge
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freetype-py               2.3.0              pyhd8ed1ab_0    conda-forge
frozenlist                1.7.0           py311h52bc045_0    conda-forge
fsspec                    2025.12.0          pyhd8ed1ab_0    conda-forge
gast                      0.7.0              pyhd8ed1ab_0    conda-forge
giflib                    5.2.2                hd590300_0    conda-forge
gmp                       6.3.0                hac33072_2    conda-forge
gmpy2                     2.2.1           py311h92a432a_2    conda-forge
gmso                      0.13.0             pyhd8ed1ab_0    conda-forge
google-pasta              0.2.0              pyhd8ed1ab_2    conda-forge
greenlet                  3.3.0           py311h1ddb823_0    conda-forge
grpcio                    1.62.2          py311ha6695c7_0    conda-forge
h11                       0.16.0             pyhd8ed1ab_0    conda-forge
h2                        4.3.0              pyhcf101f3_0    conda-forge
h5py                      3.13.0          nompi_py311hb639ac4_100    conda-forge
hdf4                      4.2.15               h2a13503_7    conda-forge
hdf5                      1.14.3          nompi_h2d575fe_109    conda-forge
hpack                     4.1.0              pyhd8ed1ab_0    conda-forge
httpcore                  1.0.9              pyh29332c3_0    conda-forge
httpx                     0.28.1             pyhd8ed1ab_0    conda-forge
hyperframe                6.1.0              pyhd8ed1ab_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.11               pyhd8ed1ab_0    conda-forge
importlib-metadata        8.7.0              pyhe01879c_1    conda-forge
importlib_resources       6.5.2              pyhd8ed1ab_0    conda-forge
ipykernel                 7.1.0              pyha191276_0    conda-forge
ipython                   9.8.0              pyh53cf698_0    conda-forge
ipython_pygments_lexers   1.1.1              pyhd8ed1ab_0    conda-forge
ipywidgets                8.0.4                    pypi_0    pypi
isoduration               20.11.0            pyhd8ed1ab_1    conda-forge
jedi                      0.19.2             pyhd8ed1ab_1    conda-forge
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joblib                    1.5.2              pyhd8ed1ab_0    conda-forge
json5                     0.12.1             pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0              pyhcf101f3_3    conda-forge
jsonschema                4.25.1             pyhe01879c_0    conda-forge
jsonschema-specifications 2025.9.1           pyhcf101f3_0    conda-forge
jsonschema-with-format-nongpl 4.25.1               he01879c_0    conda-forge
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jupyter_client            8.7.0              pyhcf101f3_0    conda-forge
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keras                     3.11.2             pyh753f3f9_0    conda-forge
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krb5                      1.21.3               h659f571_0    conda-forge
lammps                    2024.8.29.0.0            pypi_0    pypi
lark                      1.3.1              pyhd8ed1ab_0    conda-forge
lcms2                     2.17                 h717163a_0    conda-forge
ld_impl_linux-64          2.45            default_hbd61a6d_104    conda-forge
lerc                      4.0.0                h0aef613_1    conda-forge
libabseil                 20240116.2      cxx17_he02047a_1    conda-forge
libaec                    1.1.4                h3f801dc_0    conda-forge
libblas                   3.9.0            20_linux64_mkl    conda-forge
libbrotlicommon           1.2.0                hb03c661_1    conda-forge
libbrotlidec              1.2.0                hb03c661_1    conda-forge
libbrotlienc              1.2.0                hb03c661_1    conda-forge
libcblas                  3.9.0            20_linux64_mkl    conda-forge
libcufft                  12.1.0.31            hecca717_0    conda-forge
libcurl                   8.17.0               h4e3cde8_1    conda-forge
libdeflate                1.25                 h17f619e_0    conda-forge
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libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.7.3                hecca717_0    conda-forge
libffi                    3.5.2                h9ec8514_0    conda-forge
libflint                  3.2.2                h754cb6e_0    conda-forge
libfreetype               2.14.1               ha770c72_0    conda-forge
libfreetype6              2.14.1               h73754d4_0    conda-forge
libgcc                    15.2.0              he0feb66_16    conda-forge
libgcc-ng                 15.2.0              h69a702a_16    conda-forge
libgfortran               15.2.0              h69a702a_16    conda-forge
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libglib                   2.86.3               h6548e54_0    conda-forge
libgomp                   15.2.0              he0feb66_16    conda-forge
libgrpc                   1.62.2               h15f2491_0    conda-forge
libhwloc                  2.11.2          default_he43201b_1000    conda-forge
libiconv                  1.18                 h3b78370_2    conda-forge
libjpeg-turbo             3.1.2                hb03c661_0    conda-forge
liblapack                 3.9.0            20_linux64_mkl    conda-forge
liblapacke                3.9.0            20_linux64_mkl    conda-forge
liblzma                   5.8.1                hb9d3cd8_2    conda-forge
liblzma-devel             5.8.1                hb9d3cd8_2    conda-forge
libnetcdf                 4.9.2           nompi_h135f659_114    conda-forge
libnghttp2                1.67.0               had1ee68_0    conda-forge
libnsl                    2.0.1                hb9d3cd8_1    conda-forge
libpng                    1.6.53               h421ea60_0    conda-forge
libprotobuf               4.25.3               hd5b35b9_1    conda-forge
libre2-11                 2023.09.01           h5a48ba9_2    conda-forge
libsodium                 1.0.20               h4ab18f5_0    conda-forge
libsqlite                 3.51.1               h0c1763c_0    conda-forge
libssh2                   1.11.1               hcf80075_0    conda-forge
libstdcxx                 15.2.0              h934c35e_16    conda-forge
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libuuid                   2.41.2               h5347b49_1    conda-forge
libuv                     1.51.0               hb03c661_1    conda-forge
libwebp-base              1.6.0                hd42ef1d_0    conda-forge
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libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.7               h4c95cb1_3    conda-forge
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lightning-utilities       0.15.2             pyhd8ed1ab_0    conda-forge
llvm-openmp               21.1.7               h4922eb0_0    conda-forge
lxml                      5.3.0           py311hcfaa980_2    conda-forge
lz4-c                     1.10.0               h5888daf_1    conda-forge
markdown                  3.10               pyhcf101f3_1    conda-forge
markdown-it-py            4.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                3.0.3           py311h3778330_0    conda-forge
matplotlib-base           3.10.8          py311h0f3be63_0    conda-forge
matplotlib-inline         0.2.1              pyhd8ed1ab_0    conda-forge
mbuild                    1.2.0              pyhd8ed1ab_0    conda-forge
mda-xdrlib                0.2.0              pyhd8ed1ab_1    conda-forge
mdtraj                    1.11.0          np2py311hb255e1c_3    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_1    conda-forge
metis                     5.1.1                h59595ed_2    conda-forge
mistune                   3.1.4              pyhcf101f3_0    conda-forge
mkl                       2023.2.0         ha770c72_50498    conda-forge
ml_dtypes                 0.3.2           py311h320fe9a_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
mpc                       1.3.1                h24ddda3_1    conda-forge
mpfr                      4.2.1                h90cbb55_3    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_1    conda-forge
multidict                 6.6.3           py311h2dc5d0c_0    conda-forge
munkres                   1.1.4              pyhd8ed1ab_1    conda-forge
namex                     0.1.0              pyhd8ed1ab_0    conda-forge
nbclient                  0.10.2             pyhd8ed1ab_0    conda-forge
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nbformat                  5.10.4             pyhd8ed1ab_1    conda-forge
ncurses                   6.5                  h2d0b736_3    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_1    conda-forge
netcdf-fortran            4.6.1           nompi_h22f9119_108    conda-forge
networkx                  3.6.1              pyhcf101f3_0    conda-forge
nglview                   3.0.6                    pypi_0    pypi
notebook                  7.5.0              pyhcf101f3_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_1    conda-forge
numexpr                   2.10.1          mkl_py311h8e25920_2    conda-forge
numpy                     1.26.4          py311h64a7726_0    conda-forge
ocl-icd                   2.3.3                hb9d3cd8_0    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
openbabel                 3.1.1           py311h8b422cb_9    conda-forge
opencl-headers            2025.06.13           h5888daf_0    conda-forge
openff-amber-ff-ports     2025.09.0          pyhd8ed1ab_0    conda-forge
openff-forcefields        2025.10.1          pyhd8ed1ab_0    conda-forge
openff-interchange        0.4.9              pyhd8ed1ab_0    conda-forge
openff-interchange-base   0.4.9              pyhd8ed1ab_0    conda-forge
openff-nagl               0.5.4              pyhd8ed1ab_1    conda-forge
openff-nagl-base          0.5.4              pyhd8ed1ab_1    conda-forge
openff-nagl-models        2025.9.0           pyhd8ed1ab_0    conda-forge
openff-toolkit            0.18.0             pyhd8ed1ab_0    conda-forge
openff-toolkit-base       0.18.0             pyhd8ed1ab_0    conda-forge
openff-units              0.3.1              pyhd8ed1ab_2    conda-forge
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zlib-ng                   2.2.5                hde8ca8f_1    conda-forge
zstd                      1.5.7                hb78ec9c_6    conda-forge

Additional context
The MRE above with diatomic nitrogen ("N#N") runs without a hitch and is able to parameterize. I didn't spot anything which looked like a Bond constraint for O2 after a cursory search for SMIRKS like "[#8X1..." through openff-2.0.0.offxml, but I don't want to make any hasty conclusions. I'd like to be sure this is a genuine bug and not just a misunderstanding on my part, but can Sage really not parameterize molecular oxygen?

[j-wags]

Transferred to openff-forcefields, since it's a scope/science question.

I think this is intentional - I don't think we have training data on O2 (or CO2 or N2 for that matter). The reason N2 works could just be an unintentional side effect of supporting particular charge states of azides (like hydrazoic acid), and CO2 may be unintentionally covered by some carboxylic acid parameters.

We might consider this as something we can fix in SMIRKS (that is, test to ensure these gases AREN'T parameterizable) in a future force field.

[lilyminium]

What Jeff said is correct -- we don't currently really train or benchmark to gases, and the other gases you mention can be assigned parameters because they are serendipitiously similar to other functional groups within the force field. These parameters aren't likely to be very well-suited -- for example, I'd suspect that the N#N bond winds up a bit longer than you want for N2 due to fitting to azides. I like your idea of making the SMIRKS a bit more strict, Jeff.

[timbernat]

Thanks for the insightful responses! In the back of my mind I was worried the CO2 might've been mis-parameterized in the manner described, so it's good to have that corroborated, if a bit unfortunate for the study we want to run.

something we can fix in SMIRKS (that is, test to ensure these gases AREN'T parameterizable) in a future force field.

I'm not sure I completely understand what's being suggested; is it that the forcefield would check no cover of the small molecule gas SMIRKS by the SMIRKs defined in the offxml is possible? (e.g. check [#8X1:1]=[#6X2:2]=[#8X1:3] can't be covered)

To keep the project at hand rolling, it sounds like one option might be to compile a tiny offxml with the relevant gas parameters (namely bond + LJ for O2, and bond + angle + LJ for CO2) and supply that alongside e.g. openff-2.0.0 when initializing a ForceField. That said, I don't have the expertise (or frankly, the desire) to fit parameters for these simple gases against something like the Sage training set. Are there any recommended sources for well-validated parameters for such from prior art (e.g. GAFF)?

[lilyminium]

is it that the forcefield would check no cover of the small molecule gas SMIRKS by the SMIRKs defined in the offxml is possible?

Yes I think that is what Jeff means -- e.g. to go back to the N#N case we could modify the SMIRKS parameter to specify that at least one N needs multiple bonds (perhaps something like [#7!X1:1]#[#7], for example).

Your plan sounds like the easiest way to move forward, yes. I don't know what would be best off the top of my head -- I think you might want to look around the literature for similar studies to see what they did. This paper from the Heinz lab does develop parameters for the gases you've mentioned that they claim are compatible with AMBER; another way I've seen it done is to use constraints for the bonds/angles and only model the nonbondeds.