UnassignedChemistryInPDBError: Can't make topology from a small molecule box with small molecule and lipid membrane

[HoaSoup]

Describe the bug
Hello, I was trying to re-construct an OpenMM topology to continue a previously-run simulation. The topology contains a protein (chain A) in complex with a small molecule (chain B, called UNK in the pdb) and embedded in a lipid membrane (chain C, called DOP in the pdb file). Here's the complex file and the ligand file. After the topology is successfully reconstructed, I will load it to an OpenMM modeller object, then load the modeller to simulation object and finally reinitialize the simulation with an OpenMM checkpoint file.

To Reproduce
Here's my code:

input_pdb_file = "/path/to/complex.pdb"
input_sdf_file = "/path/to/ligand.sdf"
complex_off_topology = offtoolkit.Topology.from_pdb(get_data_file_path(input_pdb_file, package_name="openff.toolkit"), unique_molecules=[offtoolkit.Molecule.from_file(input_sdf_file)])

This code generated the following error

Output

Exception has occurred: UnassignedChemistryInPDBError
Some bonds or atoms in the input could not be identified.

Hint: The following residue names with unassigned atoms were not found in the substructure library. While the OpenFF Toolkit identifies residues by matching chemical substructures rather than by residue name, it currently only supports the 20 'canonical' amino acids.
    DOP


Hint: The following residues were assigned names that do not match the residue name in the input, or could not be assigned residue names at all. This may indicate that atoms are missing from the input or some other error. The OpenFF Toolkit requires all atoms, including hydrogens, to be explicit in the input to avoid ambiguities in protonation state or bond order:
    Input residue B:UNK#0001 contains atoms matching substructures {'UNIQUE_MOLECULE'}
    Input residue C:DOP#0001 contains atoms matching substructures {'NO MATCH'}
    Input residue C:DOP#0002 contains atoms matching substructures {'NO MATCH'}
    Input residue C:DOP#0003 contains atoms matching substructures {'NO MATCH'}
...
Error: The following 67068 atoms exist in the input but could not be assigned chemical information from the substructure library:
    Atom  6546 (N) in residue C:DOP#0001
    Atom  6547 (C12) in residue C:DOP#0001
    Atom  6548 (C13) in residue C:DOP#0001
    Atom  6549 (C14) in residue C:DOP#0001
    Atom  6550 (C15) in residue C:DOP#0001
    Atom  6551 (H12A) in residue C:DOP#0001
    Atom  6552 (H12B) in residue C:DOP#0001
    Atom  6553 (H13A) in residue C:DOP#0001
    Atom  6554 (H13B) in residue C:DOP#0001
    Atom  6555 (H13C) in residue C:DOP#0001
    Atom  6556 (H14A) in residue C:DOP#0001
    Atom  6557 (H14B) in residue C:DOP#0001
    Atom  6558 (H14C) in residue C:DOP#0001
    Atom  6559 (H15A) in residue C:DOP#0001
    Atom  6560 (H15B) in residue C:DOP#0001
...

The error message from this point on is too long (67000s lines more), so I stopped scrolling. I don't know if there are more errors, but let's just solve these above first and see if there are still more to fix.

Computing environment (please complete the following information):

• Operating system: Ubuntu 24.04.4 LTS (GNU/Linux 6.8.0-106-generic x86_64)
• Output of running conda list:

# packages in environment at /home/hoalt/tool/miniforge3/envs/masterpipeline:
#
# Name                              Version          Build                              Channel
_openmp_mutex                       4.5              7_kmp_llvm                         conda-forge
alabaster                           1.0.0            pyhd8ed1ab_1                       conda-forge
alsa-lib                            1.2.15.3         hb03c661_0                         conda-forge
ambertools                          24.8             cuda_None_nompi_py310h834fefc_101  conda-forge
amberutils                          21.0             pypi_0                             pypi
annotated-types                     0.7.0            pyhd8ed1ab_1                       conda-forge
anyio                               4.12.1           pyhcf101f3_0                       conda-forge
argon2-cffi                         25.1.0           pyhd8ed1ab_0                       conda-forge
argon2-cffi-bindings                25.1.0           py310h7c4b9e2_2                    conda-forge
arpack                              3.9.1            nompi_hf03ea27_102                 conda-forge
arrow                               1.4.0            pyhcf101f3_0                       conda-forge
asttokens                           3.0.1            pyhd8ed1ab_0                       conda-forge
async-lru                           2.1.0            pyhcf101f3_0                       conda-forge
attr                                2.5.2            h39aace5_0                         conda-forge
attrs                               25.4.0           pyhcf101f3_1                       conda-forge
aws-c-auth                          0.9.0            h92a005d_16                        conda-forge
aws-c-cal                           0.9.2            he7b75e1_1                         conda-forge
aws-c-common                        0.12.4           hb03c661_0                         conda-forge
aws-c-compression                   0.3.1            h92c474e_6                         conda-forge
aws-c-event-stream                  0.5.5            h0c2b49e_1                         conda-forge
aws-c-http                          0.10.2           hee85082_3                         conda-forge
aws-c-io                            0.21.0           h1d8da38_1                         conda-forge
aws-c-mqtt                          0.13.1           h46c1de9_4                         conda-forge
aws-c-s3                            0.8.3            h9cdc349_1                         conda-forge
aws-c-sdkutils                      0.2.4            h92c474e_1                         conda-forge
aws-checksums                       0.2.7            h92c474e_2                         conda-forge
aws-crt-cpp                         0.32.10          h186f887_3                         conda-forge
aws-sdk-cpp                         1.11.510         h379b65b_14                        conda-forge
azure-core-cpp                      1.14.0           h5cfcd09_0                         conda-forge
azure-identity-cpp                  1.10.0           h113e628_0                         conda-forge
azure-storage-blobs-cpp             12.13.0          h3cf044e_1                         conda-forge
azure-storage-common-cpp            12.8.0           h736e048_1                         conda-forge
azure-storage-files-datalake-cpp    12.12.0          ha633028_1                         conda-forge
babel                               2.18.0           pyhcf101f3_0                       conda-forge
beautifulsoup4                      4.14.3           pyha770c72_0                       conda-forge
biopython                           1.85             pypi_0                             pypi
bleach                              6.3.0            pyhcf101f3_1                       conda-forge
bleach-with-css                     6.3.0            hbca2aae_1                         conda-forge
blosc                               1.21.6           he440d0b_1                         conda-forge
bokeh                               3.8.2            pyhd8ed1ab_0                       conda-forge
brotli                              1.1.0            hb03c661_4                         conda-forge
brotli-bin                          1.1.0            hb03c661_4                         conda-forge
brotli-python                       1.1.0            py310hea6c23e_4                    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                            2.15.2           h3122c55_1                         conda-forge
ca-certificates                     2026.1.4         hbd8a1cb_0                         conda-forge
cached-property                     1.5.2            hd8ed1ab_1                         conda-forge
cached_property                     1.5.2            pyha770c72_1                       conda-forge
cachetools                          7.0.1            pyhd8ed1ab_0                       conda-forge
cairo                               1.18.4           h3394656_0                         conda-forge
cctbx-base                          2026.1           pypi_0                             pypi
cdpkit                              1.2.3            pypi_0                             pypi
cerberus                            1.3.7            pypi_0                             pypi
certifi                             2025.6.15        pypi_0                             pypi
cffi                                2.0.0            py310he7384ee_1                    conda-forge
cftime                              1.6.4.post1      pypi_0                             pypi
charset-normalizer                  3.4.4            pyhd8ed1ab_0                       conda-forge
chem_data                           2026.1           pyh3b8433e_0                       chem_data
click                               8.3.1            pyh8f84b5b_1                       conda-forge
cloudpickle                         3.1.2            pyhcf101f3_1                       conda-forge
colorama                            0.4.6            pyhd8ed1ab_1                       conda-forge
colorlog                            6.9.0            pypi_0                             pypi
comm                                0.2.3            pyhe01879c_0                       conda-forge
contourpy                           1.3.2            py310h3788b33_0                    conda-forge
cudatoolkit                         11.8.0           h4ba93d1_13                        conda-forge
cycler                              0.12.1           pyhcf101f3_2                       conda-forge
cyrus-sasl                          2.1.28           hd9c7081_0                         conda-forge
cytoolz                             1.1.0            py310h7c4b9e2_1                    conda-forge
dask                                2026.1.2         pyhcf101f3_0                       conda-forge
dask-core                           2026.1.2         pyhcf101f3_0                       conda-forge
dbus                                1.16.2           h24cb091_1                         conda-forge
debugpy                             1.8.20           py310h25320af_0                    conda-forge
decorator                           5.2.1            pyhd8ed1ab_0                       conda-forge
defusedxml                          0.7.1            pyhd8ed1ab_0                       conda-forge
delphi4py                           1.3.0            pypi_0                             pypi
dill                                0.4.0            pypi_0                             pypi
distributed                         2026.1.2         pyhcf101f3_0                       conda-forge
dkh                                 1.2              ha94c79b_3                         conda-forge
docopt                              0.6.2            pypi_0                             pypi
docutils                            0.21.2           pyhd8ed1ab_1                       conda-forge
edgembar                            3.0              pypi_0                             pypi
exceptiongroup                      1.3.0            pypi_0                             pypi
executing                           2.2.1            pyhd8ed1ab_0                       conda-forge
fftw                                3.3.10           nompi_h3b011a4_111                 conda-forge
filelock                            3.23.0           pyhd8ed1ab_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                           4.61.1           py310h3406613_0                    conda-forge
fqdn                                1.5.1            pyhd8ed1ab_1                       conda-forge
freesasa                            2.2.1            pypi_0                             pypi
freetype                            2.14.1           ha770c72_0                         conda-forge
freetype-py                         2.3.0            pyhd8ed1ab_0                       conda-forge
fsspec                              2026.2.0         pyhd8ed1ab_0                       conda-forge
future                              1.0.0            pyhd8ed1ab_2                       conda-forge
gau2grid                            2.0.8            hb9d3cd8_0                         conda-forge
gemmi                               0.7.4            py310h591710a_0                    conda-forge
gflags                              2.2.2            h5888daf_1005                      conda-forge
glew                                2.1.0            h9c3ff4c_2                         conda-forge
glib                                2.86.3           h5192d8d_1                         conda-forge
glib-tools                          2.86.3           hf516916_1                         conda-forge
glm                                 1.0.1            hdd259ec_0                         conda-forge
glog                                0.7.1            hbabe93e_0                         conda-forge
gputil                              1.4.0            pypi_0                             pypi
graphite2                           1.3.14           hecca717_2                         conda-forge
greenlet                            3.3.1            py310h25320af_1                    conda-forge
griddataformats                     1.0.2            pyhd8ed1ab_1                       conda-forge
gsd                                 4.0.0            py310h7c4b9e2_1                    conda-forge
gst-plugins-base                    1.24.11          h651a532_0                         conda-forge
gstreamer                           1.24.11          hc37bda9_0                         conda-forge
h11                                 0.16.0           pyhcf101f3_1                       conda-forge
h2                                  4.3.0            pyhcf101f3_0                       conda-forge
h5py                                3.12.1           nompi_py310hacc6608_103            conda-forge
haddock3                            2025.5.0         pypi_0                             pypi
harfbuzz                            12.2.0           h15599e2_0                         conda-forge
hdf4                                4.2.15           h2a13503_7                         conda-forge
hdf5                                1.14.4           nompi_h2d575fe_105                 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                                 75.1             he02047a_0                         conda-forge
idna                                3.11             pyhd8ed1ab_0                       conda-forge
imagesize                           1.4.1            pyhd8ed1ab_0                       conda-forge
importlib-metadata                  8.7.0            pyhe01879c_1                       conda-forge
importlib_resources                 6.5.2            pyhd8ed1ab_0                       conda-forge
iniconfig                           2.1.0            pypi_0                             pypi
ipykernel                           7.2.0            pyha191276_1                       conda-forge
ipython                             8.37.0           pyh8f84b5b_0                       conda-forge
ipywidgets                          8.1.8            pyhd8ed1ab_0                       conda-forge
isoduration                         20.11.0          pyhd8ed1ab_1                       conda-forge
jax                                 0.6.2            pyhd8ed1ab_0                       conda-forge
jaxlib                              0.6.2            cpu_py310h772e2ea_1                conda-forge
jedi                                0.19.2           pyhd8ed1ab_1                       conda-forge
jinja2                              3.1.6            pyhcf101f3_1                       conda-forge
joblib                              1.5.3            pyhd8ed1ab_0                       conda-forge
json5                               0.13.0           pyhd8ed1ab_0                       conda-forge
jsonargparse                        4.40.0           pypi_0                             pypi
jsonpickle                          4.1.1            pypi_0                             pypi
jsonpointer                         3.0.0            pyhcf101f3_3                       conda-forge
jsonschema                          4.26.0           pyhcf101f3_0                       conda-forge
jsonschema-specifications           2025.9.1         pyhcf101f3_0                       conda-forge
jsonschema-with-format-nongpl       4.26.0           hcf101f3_0                         conda-forge
jupyter-lsp                         2.3.0            pyhcf101f3_0                       conda-forge
jupyter_client                      8.8.0            pyhcf101f3_0                       conda-forge
jupyter_core                        5.9.1            pyhc90fa1f_0                       conda-forge
jupyter_events                      0.12.0           pyhe01879c_0                       conda-forge
jupyter_server                      2.17.0           pyhcf101f3_0                       conda-forge
jupyter_server_terminals            0.5.4            pyhcf101f3_0                       conda-forge
jupyterlab                          4.5.4            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
kernel-headers_linux-64             6.12.0           he073ed8_5                         conda-forge
keyutils                            1.6.3            hb9d3cd8_0                         conda-forge
kiwisolver                          1.4.9            py310haaf941d_2                    conda-forge
krb5                                1.21.3           h659f571_0                         conda-forge
lame                                3.100            h166bdaf_1003                      conda-forge
lark                                1.3.1            pyhd8ed1ab_0                       conda-forge
lcms2                               2.18             h0c24ade_0                         conda-forge
ld_impl_linux-64                    2.45.1           default_hbd61a6d_101               conda-forge
lerc                                4.0.0            h0aef613_1                         conda-forge
libabseil                           20250127.1       cxx17_hbbce691_0                   conda-forge
libaec                              1.1.5            h088129d_0                         conda-forge
libarrow                            20.0.0           h019e7cd_8_cuda                    conda-forge
libarrow-acero                      20.0.0           hb826db4_8_cuda                    conda-forge
libarrow-dataset                    20.0.0           hb826db4_8_cuda                    conda-forge
libarrow-substrait                  20.0.0           h69308b4_8_cuda                    conda-forge
libblas                             3.9.0            37_h5875eb1_mkl                    conda-forge
libboost                            1.86.0           hed09d94_4                         conda-forge
libboost-python                     1.86.0           py310hc563356_5                    conda-forge
libbrotlicommon                     1.1.0            hb03c661_4                         conda-forge
libbrotlidec                        1.1.0            hb03c661_4                         conda-forge
libbrotlienc                        1.1.0            hb03c661_4                         conda-forge
libcap                              2.77             h3ff7636_0                         conda-forge
libcblas                            3.9.0            37_hfef963f_mkl                    conda-forge
libclang-cpp20.1                    20.1.8           default_h99862b1_8                 conda-forge
libclang13                          21.1.0           default_h746c552_1                 conda-forge
libcrc32c                           1.1.2            h9c3ff4c_0                         conda-forge
libcups                             2.3.3            hb8b1518_5                         conda-forge
libcurl                             8.18.0           h4e3cde8_0                         conda-forge
libdeflate                          1.25             h17f619e_0                         conda-forge
libdrm                              2.4.125          hb03c661_1                         conda-forge
libecpint                           1.0.7            h981d57b_12                        conda-forge
libedit                             3.1.20250104     pl5321h7949ede_0                   conda-forge
libegl                              1.7.0            ha4b6fd6_2                         conda-forge
libev                               4.33             hd590300_2                         conda-forge
libevent                            2.1.12           hf998b51_1                         conda-forge
libexpat                            2.7.3            hecca717_0                         conda-forge
libfabric                           2.4.0            ha770c72_1                         conda-forge
libfabric1                          2.4.0            h8f87c3e_1                         conda-forge
libffi                              3.5.2            h3435931_0                         conda-forge
libflac                             1.5.0            he200343_1                         conda-forge
libfreetype                         2.14.1           ha770c72_0                         conda-forge
libfreetype6                        2.14.1           h73754d4_0                         conda-forge
libgcc                              15.2.0           he0feb66_17                        conda-forge
libgcc-ng                           15.2.0           h69a702a_17                        conda-forge
libgfortran                         15.2.0           h69a702a_17                        conda-forge
libgfortran5                        15.2.0           h68bc16d_17                        conda-forge
libgl                               1.7.0            ha4b6fd6_2                         conda-forge
libglib                             2.86.3           h6548e54_1                         conda-forge
libglu                              9.0.3            h5888daf_1                         conda-forge
libglvnd                            1.7.0            ha4b6fd6_2                         conda-forge
libglx                              1.7.0            ha4b6fd6_2                         conda-forge
libgomp                             15.2.0           he0feb66_17                        conda-forge
libgoogle-cloud                     2.36.0           hc4361e1_1                         conda-forge
libgoogle-cloud-storage             2.36.0           h0121fbd_1                         conda-forge
libgrpc                             1.71.0           h8e591d7_1                         conda-forge
libhwloc                            2.12.1           default_h3d81e11_1000              conda-forge
libiconv                            1.18             h3b78370_2                         conda-forge
libint                              2.13.1           h83f5b4b_0                         conda-forge
libjpeg-turbo                       3.1.2            hb03c661_0                         conda-forge
liblapack                           3.9.0            37_h5e43f62_mkl                    conda-forge
libllvm20                           20.1.8           hecd9e04_0                         conda-forge
libllvm21                           21.1.0           hecd9e04_0                         conda-forge
liblzma                             5.8.2            hb03c661_0                         conda-forge
libnetcdf                           4.9.2            nompi_h5ddbaa4_116                 conda-forge
libnghttp2                          1.67.0           had1ee68_0                         conda-forge
libnl                               3.11.0           hb9d3cd8_0                         conda-forge
libnsl                              2.0.1            hb9d3cd8_1                         conda-forge
libntlm                             1.8              hb9d3cd8_0                         conda-forge
libogg                              1.3.5            hd0c01bc_1                         conda-forge
libopengl                           1.7.0            ha4b6fd6_2                         conda-forge
libopentelemetry-cpp                1.21.0           hd1b1c89_0                         conda-forge
libopentelemetry-cpp-headers        1.21.0           ha770c72_0                         conda-forge
libopus                             1.6.1            h280c20c_0                         conda-forge
libparquet                          20.0.0           h3f30f2e_8_cuda                    conda-forge
libpciaccess                        0.18             hb9d3cd8_0                         conda-forge
libpcm                              1.2.3            hdca9e5a_15                        conda-forge
libpng                              1.6.55           h421ea60_0                         conda-forge
libpq                               17.7             h5c52fec_1                         conda-forge
libprotobuf                         5.29.3           h7460b1f_3                         conda-forge
librdkit                            2025.03.6        h3c5c181_0                         conda-forge
libre2-11                           2025.06.26       hba17884_0                         conda-forge
libsndfile                          1.2.2            hc7d488a_2                         conda-forge
libsodium                           1.0.20           h4ab18f5_0                         conda-forge
libsqlite                           3.51.2           h0c1763c_0                         conda-forge
libssh2                             1.11.1           hcf80075_0                         conda-forge
libstdcxx                           15.2.0           h934c35e_17                        conda-forge
libstdcxx-ng                        15.2.0           hdf11a46_17                        conda-forge
libsvm                              337              hecca717_0                         conda-forge
libsystemd0                         259.1            h6569c3e_0                         conda-forge
libthrift                           0.21.0           h0e7cc3e_0                         conda-forge
libtiff                             4.7.1            h9d88235_1                         conda-forge
libudev1                            259.1            h6569c3e_0                         conda-forge
libutf8proc                         2.10.0           h202a827_0                         conda-forge
libuuid                             2.41.3           h5347b49_0                         conda-forge
libvorbis                           1.3.7            h54a6638_2                         conda-forge
libwebp-base                        1.6.0            hd42ef1d_0                         conda-forge
libxc-c                             7.0.0            cpu_h75f4f88_6                     conda-forge
libxcb                              1.17.0           h8a09558_0                         conda-forge
libxcrypt                           4.4.36           hd590300_1                         conda-forge
libxkbcommon                        1.11.0           he8b52b9_0                         conda-forge
libxml2                             2.13.9           h04c0eec_0                         conda-forge
libxslt                             1.1.43           h7a3aeb2_0                         conda-forge
libzip                              1.11.2           h6991a6a_0                         conda-forge
libzlib                             1.3.1            hb9d3cd8_2                         conda-forge
llvm-openmp                         21.1.8           h4922eb0_0                         conda-forge
llvmlite                            0.46.0           py310hee1c697_0                    conda-forge
locket                              1.0.0            pyhd8ed1ab_0                       conda-forge
lxml                                6.0.2            py310h93f867a_0                    conda-forge
lz4                                 4.4.5            py310hde1b0b5_1                    conda-forge
lz4-c                               1.10.0           h5888daf_1                         conda-forge
markupsafe                          3.0.3            py310h3406613_0                    conda-forge
matplotlib-base                     3.10.8           py310hfde16b3_0                    conda-forge
matplotlib-inline                   0.2.1            pyhd8ed1ab_0                       conda-forge
md                                  0.1.0            pypi_0                             pypi
mda-xdrlib                          0.2.0            pyhd8ed1ab_1                       conda-forge
mdanalysis                          2.9.0            py310h5eaa309_1                    conda-forge
mdtraj                              1.10.3           py310h4cdbd58_0                    conda-forge
mistune                             3.2.0            pyhcf101f3_0                       conda-forge
mkl                                 2024.2.2         ha770c72_17                        conda-forge
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mmpbsa-py                           16.0             pypi_0                             pypi
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mpi                                 1.0.1            mpich                              conda-forge
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pyarrow                             20.0.0           py310hff52083_2                    conda-forge
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python                              3.10.19          h3c07f61_3_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-json-logger                  2.0.7            pyhd8ed1ab_0                       conda-forge
python_abi                          3.10             8_cp310                            conda-forge
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rdma-core                           61.0             h192683f_0                         conda-forge
re2                                 2025.06.26       h9925aae_0                         conda-forge
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referencing                         0.37.0           pyhcf101f3_0                       conda-forge
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rfc3339-validator                   0.1.4            pyhd8ed1ab_1                       conda-forge
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sander                              22.0             pypi_0                             pypi
scikit-learn                        1.7.2            py310h228f341_0                    conda-forge
scipy                               1.15.3           pypi_0                             pypi
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seaborn                             0.13.2           hd8ed1ab_3                         conda-forge
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setuptools                          80.10.2          pypi_0                             pypi
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smirnoff99frosst                    1.1.0.1          pyhd8ed1ab_0                       conda-forge
snappy                              1.2.2            h03e3b7b_1                         conda-forge
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snowballstemmer                     3.0.1            pyhd8ed1ab_0                       conda-forge
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sphinxcontrib-devhelp               2.0.0            pyhd8ed1ab_1                       conda-forge
sphinxcontrib-htmlhelp              2.1.0            pyhd8ed1ab_1                       conda-forge
sphinxcontrib-jsmath                1.0.1            pyhd8ed1ab_1                       conda-forge
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sphinxcontrib-serializinghtml       1.1.10           pyhd8ed1ab_1                       conda-forge
sqlalchemy                          2.0.46           py310h139afa4_1                    conda-forge
stack_data                          0.6.3            pyhd8ed1ab_1                       conda-forge
statsmodels                         0.14.6           py310hf779ad0_0                    conda-forge
sysroot_linux-64                    2.39             hc4b9eeb_5                         conda-forge
tbb                                 2021.13.0        h8d10470_4                         conda-forge
tblib                               3.2.2            pyhcf101f3_0                       conda-forge
tenacity                            9.1.2            pypi_0                             pypi
terminado                           0.18.1           pyhc90fa1f_1                       conda-forge
threadpoolctl                       3.6.0            pyhecae5ae_0                       conda-forge
tidynamics                          1.1.2            pyhd8ed1ab_0                       conda-forge
tinycss2                            1.4.0            pyhd8ed1ab_0                       conda-forge
tinydb                              4.8.2            pyhd8ed1ab_1                       conda-forge
tk                                  8.6.13           noxft_h366c992_103                 conda-forge
toml                                0.10.2           pyhcf101f3_3                       conda-forge
tomli                               2.2.1            pypi_0                             pypi
toolz                               1.1.0            pyhd8ed1ab_1                       conda-forge
tornado                             6.5.4            py310ha78b2d2_0                    conda-forge
tqdm                                4.67.1           pypi_0                             pypi
traitlets                           5.14.3           pyhd8ed1ab_1                       conda-forge
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ucx                                 1.19.1           h567e125_0                         conda-forge
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urllib3                             2.5.0            pyhd8ed1ab_0                       conda-forge
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wcwidth                             0.6.0            pyhd8ed1ab_0                       conda-forge
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webencodings                        0.5.1            pyhd8ed1ab_3                       conda-forge
websocket-client                    1.9.0            pyhd8ed1ab_0                       conda-forge
wheel                               0.46.3           pyhd8ed1ab_0                       conda-forge
widgetsnbextension                  4.0.15           pyhd8ed1ab_0                       conda-forge
xcb-util                            0.4.1            h4f16b4b_2                         conda-forge
xcb-util-image                      0.4.0            hb711507_2                         conda-forge
xcb-util-keysyms                    0.4.1            hb711507_0                         conda-forge
xcb-util-renderutil                 0.3.10           hb711507_0                         conda-forge
xcb-util-wm                         0.4.2            hb711507_0                         conda-forge
xkeyboard-config                    2.46             hb03c661_0                         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                         1.8.13           he1eb515_0                         conda-forge
xorg-libxau                         1.0.12           hb03c661_1                         conda-forge
xorg-libxcomposite                  0.4.7            hb03c661_0                         conda-forge
xorg-libxdamage                     1.1.6            hb9d3cd8_0                         conda-forge
xorg-libxdmcp                       1.1.5            hb03c661_1                         conda-forge
xorg-libxext                        1.3.7            hb03c661_0                         conda-forge
xorg-libxfixes                      6.0.2            hb03c661_0                         conda-forge
xorg-libxrender                     0.9.12           hb9d3cd8_0                         conda-forge
xorg-libxshmfence                   1.3.3            hb9d3cd8_0                         conda-forge
xorg-libxt                          1.3.1            hb9d3cd8_0                         conda-forge
xorg-libxxf86vm                     1.1.7            hb03c661_0                         conda-forge
xyzservices                         2025.11.0        pyhd8ed1ab_0                       conda-forge
yaml                                0.2.5            h280c20c_3                         conda-forge
zeromq                              4.3.5            h387f397_9                         conda-forge
zict                                3.0.0            pyhd8ed1ab_1                       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
zstandard                           0.25.0           py310h139afa4_1                    conda-forge
zstd                                1.5.7            hb78ec9c_6                         conda-forge

Thank you for your help.
Best regards,
Hoa

[j-wags]

Hi @HoaSoup -

• It's not clear that you need to make an OpenFF Topology to resume the simulation:
  • if this workflow doesn't intend to change the parameterization of the system, the easiest way to checkpoint and resume an OpenMM simulation is using OpenMMs checkpoint functionality for the simulation positions/velocities, and OpenMM's XmlSerializer to save+load the OpenMM Topology and System. Reloading from PDB files will lose precision in the positions and all the velocities.
• If there IS a reason that this workflow needs to create an OpenFF Topology,
  • the error message indicates that the DOP lipids are unable to be loaded. This is because the small molecule ligand is provided in the unique_molecules list, but the DOP molecules are not. You'll need to ensure that the DOP lipids have CONECT records in the PDB file, and provide the reference molecule in the unique_molecules list. This can be made from its SMILES for simplicity, though it may take some additional work to get the protonation state to match what's in the PDB. For example:

input_pdb_file = "/path/to/complex.pdb"
input_sdf_file = "/path/to/ligand.sdf"
input_dop_smiles = "CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC[N+](C)(C)C)OC(=O)CCCCCCC/C=C\CCCCCCCC"
ligand = offtoolkit.Molecule.from_file(input_sdf_file)
dopc = offtoolkit.Molecule.from_smiles(input_dop_smiles)
complex_off_topology = offtoolkit.Topology.from_pdb(get_data_file_path(input_pdb_file, package_name="openff.toolkit"), unique_molecules=[ligand, dopc])

• I'm able to download the PDB file but not the SDF, I think the sharing setting on the SDF need to be updated to be publicly visible.

[HoaSoup]

Hi @j-wags ,

I guess the cause of my bug is that the atom naming convention for the ligand and DOPC molecules are not recognized by OpenFF.

My aim was to reconstruct an OpenMM topology object. One way to do it was through creating OpenFF topology, then converting it to OpenMM topology. But your question raised some food for thought. So, I change my approach and do this:

ligand_path = get_data_file_path("/path/to/ligand.sdf")
ligand = Molecule.from_file(ligand_path)

pdb = openmm_app.PDBFile("/path/to/pdb")
gaff = ommff_GAFFTemplateGenerator(
    molecules=[ligand],
    cache="/path/to/gaff.cache.json")

forcefield = openmm_app.forcefield.ForceField("amber14-all.xml", "amber14/tip3p.xml")
forcefield.registerTemplateGenerator(gaff.generator)
system = forcefield.createSystem(pdb.topology, nonbondedMethod=openmm_app.forcefield.NoCutoff, constraints=openmm_app.forcefield.HBonds)
integrator = openmm.LangevinMiddleIntegrator(300*ou.kelvin, 1/ou.picosecond, 0.002*ou.picoseconds)
simulation = openmm_app.simulation.Simulation(pdb.topology, system, integrator)
simulation.loadCheckpoint("/home/hoalt/code/master-pipeline/src/packages/md/tests/full_features/output/relaxation.chk")

It worked. The problem is fixed.
Thank you very much.
Best regards,
Hoa