Sage has no bonded parameters for diatomic oxygen? #140
Description
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
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
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
fqdn 1.5.1 pyhd8ed1ab_1 conda-forge
freetype 2.14.1 ha770c72_0 conda-forge
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
jinja2 3.1.6 pyhcf101f3_1 conda-forge
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
jupyter-lsp 2.3.0 pyhcf101f3_0 conda-forge
jupyter_client 8.7.0 pyhcf101f3_0 conda-forge
jupyter_core 5.9.1 pyhc90fa1f_0 conda-forge
jupyter_events 0.12.0 pyh29332c3_0 conda-forge
jupyter_server 2.17.0 pyhcf101f3_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_1 conda-forge
jupyterlab 4.5.0 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_2 conda-forge
jupyterlab_server 2.28.0 pyhcf101f3_0 conda-forge
jupyterlab_widgets 3.0.16 pyhcf101f3_1 conda-forge
keras 3.11.2 pyh753f3f9_0 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.4.9 py311h724c32c_2 conda-forge
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
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
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
libgfortran-ng 15.2.0 h69a702a_16 conda-forge
libgfortran5 15.2.0 h68bc16d_16 conda-forge
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
libstdcxx-ng 15.2.0 hdf11a46_16 conda-forge
libtiff 4.7.1 h9d88235_1 conda-forge
libtorch 2.3.1 cpu_mkl_h0bb0d08_100 conda-forge
liburing 2.7 h434a139_0 conda-forge
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
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 h4c95cb1_3 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzip 1.11.2 h6991a6a_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
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
nbconvert-core 7.16.6 pyhcf101f3_1 conda-forge
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
openff-utilities 0.1.16 pyhd8ed1ab_0 conda-forge
openjpeg 2.5.4 h55fea9a_0 conda-forge
openmm 8.4.0 py311h38e3cd7_2 conda-forge
openssl 3.6.0 h26f9b46_0 conda-forge
opt_einsum 3.4.0 pyhd8ed1ab_1 conda-forge
optree 0.18.0 py311hdf67eae_0 conda-forge
overrides 7.7.0 pyhd8ed1ab_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
packmol 20.15.1 hc8b2c43_1 conda-forge
packmol-memgen 2023.2.24 pypi_0 pypi
pandas 2.3.3 py311hed34c8f_2 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parmed 4.3.0 py311h8cc7b42_2 conda-forge
parso 0.8.5 pyhcf101f3_0 conda-forge
pcre2 10.47 haa7fec5_0 conda-forge
pdb4amber 22.0 pypi_0 pypi
perl 5.32.1 7_hd590300_perl5 conda-forge
pexpect 4.9.0 pyhd8ed1ab_1 conda-forge
pillow 12.0.0 py311h267f063_1 conda-forge
pint 0.24.4 pyhe01879c_2 conda-forge
pip 25.3 pyh8b19718_0 conda-forge
pixman 0.46.4 h54a6638_1 conda-forge
platformdirs 4.5.1 pyhcf101f3_0 conda-forge
polymerist 1.0.1+17.gdd98bd5 pypi_0 pypi
prometheus_client 0.23.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.52 pyha770c72_0 conda-forge
propcache 0.3.1 py311h2dc5d0c_0 conda-forge
protobuf 4.25.3 py311hbffca5d_1 conda-forge
psutil 7.1.3 py311haee01d2_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
ptyprocess 0.7.0 pyhd8ed1ab_1 conda-forge
pubchempy 1.0.5 pypi_0 pypi
pure_eval 0.2.3 pyhd8ed1ab_1 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_1 conda-forge
py3dmol 2.5.3 pypi_0 pypi
pycairo 1.27.0 py311h124c5f0_0 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pydantic 2.11.10 pyh3cfb1c2_0 conda-forge
pydantic-core 2.33.2 py311hdae7d1d_0 conda-forge
pyedr 0.8.0 pyhd8ed1ab_1 conda-forge
pygments 2.19.2 pyhd8ed1ab_0 conda-forge
pymsmt 22.0 pypi_0 pypi
pyparsing 3.2.5 pyhcf101f3_0 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytables 3.10.2 py311h6d53d72_2 conda-forge
python 3.11.14 hd63d673_2_cpython conda-forge
python-constraint 1.4.0 pyhff2d567_1 conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-fastjsonschema 2.21.2 pyhe01879c_0 conda-forge
python-flatbuffers 25.9.23 pyh1e1bc0e_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-symengine 0.14.0 py311h7b351a7_1 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.11 8_cp311 conda-forge
pytorch 2.3.1 cpu_mkl_py311hcb16b95_100 conda-forge
pytorch-lightning 2.6.0 pyhcf101f3_0 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.3 py311h3778330_0 conda-forge
pyzmq 27.1.0 py311h2315fbb_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
rdkit 2025.9.3 pypi_0 pypi
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.37.0 pyhcf101f3_0 conda-forge
reportlab 4.4.6 py311h49ec1c0_0 conda-forge
requests 2.32.5 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rfc3987-syntax 1.1.0 pyhe01879c_1 conda-forge
rich 14.2.0 pyhcf101f3_0 conda-forge
rlpycairo 0.4.0 pyh6c17108_0 conda-forge
rocm-core 7.0.2 h54a6638_0 conda-forge
rpds-py 0.30.0 py311h902ca64_0 conda-forge
s2n 1.5.5 h3931f03_0 conda-forge
sander 22.0 pypi_0 pypi
scipy 1.16.3 py311h1e13796_1 conda-forge
send2trash 1.8.3 pyh0d859eb_1 conda-forge
setuptools 80.9.0 pyhff2d567_0 conda-forge
signac 2.3.0 pyhd8ed1ab_0 conda-forge
signac-flow 0.29.0 pyhd8ed1ab_1 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
sleef 3.9.0 ha0421bc_0 conda-forge
snappy 1.2.2 h03e3b7b_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_2 conda-forge
soupsieve 2.8 pyhd8ed1ab_0 conda-forge
sqlalchemy 2.0.45 py311h49ec1c0_0 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
symengine 0.14.0 h064106a_1 conda-forge
sympy 1.14.0 pyh2585a3b_105 conda-forge
synced_collections 1.0.0 pyhd8ed1ab_1 conda-forge
tbb 2021.13.0 hceb3a55_1 conda-forge
tensorboard 2.16.2 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py311h97c413e_4 conda-forge
tensorflow 2.16.2 cpu_py311h6ac8430_0 conda-forge
tensorflow-base 2.16.2 cpu_py311h7888847_0 conda-forge
tensorflow-estimator 2.16.2 cpu_py311hbc9741f_0 conda-forge
termcolor 3.2.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
tinycss2 1.4.0 pypi_0 pypi
tk 8.6.13 noxft_ha0e22de_103 conda-forge
tomli 2.3.0 pyhcf101f3_0 conda-forge
torchdata 0.7.1 py311h34085b1_7 conda-forge
torchmetrics 1.8.2 pyhd8ed1ab_0 conda-forge
tornado 6.5.2 py311h49ec1c0_2 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
treelib 1.7.1 pyhd8ed1ab_0 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing-inspection 0.4.2 pyhd8ed1ab_1 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
unicodedata2 17.0.0 py311h49ec1c0_1 conda-forge
unyt 3.0.4 pyhd8ed1ab_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.6.1 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.14 pyhd8ed1ab_0 conda-forge
webcolors 25.10.0 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.9.0 pyhd8ed1ab_0 conda-forge
werkzeug 3.1.4 pyhcf101f3_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.15 pyhd8ed1ab_0 conda-forge
wrapt 2.0.1 py311h49ec1c0_1 conda-forge
xmltodict 1.0.2 pyhcf101f3_0 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xz 5.8.1 hbcc6ac9_2 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_2 conda-forge
xz-tools 5.8.1 hb9d3cd8_2 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
yarl 1.22.0 py311h3778330_0 conda-forge
zeromq 4.3.5 h387f397_9 conda-forge
zipp 3.23.0 pyhcf101f3_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.2.5 hde8ca8f_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forgeAdditional 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?