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Loading protein with C terminal NH2 cap fails #1579

Closed
chapincavender opened this issue Apr 13, 2023 · 0 comments · Fixed by #1589
Closed

Loading protein with C terminal NH2 cap fails #1579

chapincavender opened this issue Apr 13, 2023 · 0 comments · Fixed by #1589

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@chapincavender
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Describe the bug
Loading a protein with a C terminal amide (NH2) cap using Molecule.from_polymer_pdb fails.

To Reproduce
MWE using ACE-ALA-NH2
Molecule.from_polymer_pdb('ace-ala-nh2.pdb') with the following PDB file:

ATOM      1 HH33 ACE A   0      -5.284  -2.981   5.320  1.00  0.00              
ATOM      2  CH3 ACE A   0      -4.851  -3.877   5.426  1.00  0.00              
ATOM      3 HH31 ACE A   0      -5.412  -4.481   6.144  1.00  0.00              
ATOM      4 HH32 ACE A   0      -4.840  -4.406   4.474  1.00  0.00              
ATOM      5  C   ACE A   0      -3.431  -3.679   5.966  1.00  0.00              
ATOM      6  O   ACE A   0      -2.705  -2.809   5.481  1.00  0.00              
ATOM      7  N   ALA A   1      -2.983  -4.446   6.956  1.00  0.00              
ATOM      8  CA  ALA A   1      -1.682  -4.415   7.599  1.00  0.00              
ATOM      9  CB  ALA A   1      -1.818  -3.599   8.890  1.00  0.00              
ATOM     10  C   ALA A   1      -1.154  -5.834   7.868  1.00  0.00              
ATOM     11  O   ALA A   1      -1.891  -6.699   8.345  1.00  0.00              
ATOM     12  H   ALA A   1      -3.478  -5.294   6.716  1.00  0.00           H  
ATOM     13  HA  ALA A   1      -1.025  -3.946   6.994  1.00  0.00           H  
ATOM     14  HB1 ALA A   1      -2.653  -3.055   8.848  1.00  0.00           H  
ATOM     15  HB2 ALA A   1      -1.860  -4.221   9.669  1.00  0.00           H  
ATOM     16  HB3 ALA A   1      -1.028  -2.996   8.983  1.00  0.00           H  
ATOM     17  N   NH2 A   2       0.110  -6.138   7.586  1.00  0.00              
ATOM     18  HN1 NH2 A   2       0.717  -5.444   7.199  1.00  0.00              
ATOM     19  HN2 NH2 A   2       0.453  -7.061   7.761  1.00  0.00              
TER
END

Output

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: type object 'Molecule' has no attribute 'from_polymer'. Did you mean: 'from_polymer_pdb'?
>>> offmol = Molecule.from_polymer_pdb('ace-ala-nh2.pdb')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openff/utilities/utilities.py", line 80, in wrapper
    return function(*args, **kwargs)
  File "/home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openff/toolkit/topology/molecule.py", line 3855, in from_polymer_pdb
    offmol = toolkit_registry.call(
  File "/home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openff/toolkit/utils/toolkit_registry.py", line 356, in call
    raise e
  File "/home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openff/toolkit/utils/toolkit_registry.py", line 352, in call
    return method(*args, **kwargs)
  File "/home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openff/toolkit/utils/openeye_wrapper.py", line 259, in _polymer_openmm_topology_to_offmol
    oemol = self._polymer_openmm_topology_to_oemol(omm_top, substructure_dictionary)
  File "/home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openff/toolkit/utils/openeye_wrapper.py", line 362, in _polymer_openmm_topology_to_oemol
    raise UnassignedChemistryInPDBError(
openff.toolkit.utils.exceptions.UnassignedChemistryInPDBError: Some bonds or atoms in the input could not be identified.

Computing environment (please complete the following information):

  • Operating system: Ubuntu 20.04.6
  • Output of running conda list
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
alsa-lib                  1.2.8                h166bdaf_0    conda-forge
amberlite                 22.0                     pypi_0    pypi
ambertools                22.0            py310h206695f_3    conda-forge
amberutils                21.0                     pypi_0    pypi
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h5764c6d_3    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.2             pyha770c72_0    conda-forge
binutils                  2.39                 hdd6e379_1    conda-forge
binutils_impl_linux-64    2.39                 he00db2b_1    conda-forge
binutils_linux-64         2.39                h5fc0e48_11    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.3               hafa529b_0    conda-forge
boost                     1.74.0          py310h7c3ba0c_5    conda-forge
boost-cpp                 1.74.0               h75c5d50_8    conda-forge
brotli                    1.0.9                h166bdaf_8    conda-forge
brotli-bin                1.0.9                h166bdaf_8    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1005    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
c-compiler                1.5.2                h0b41bf4_0    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.3.0              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            ha61ee94_1014    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_3    conda-forge
cftime                    1.6.2           py310hde88566_1    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge
cmake                     3.26.0               h077f3f9_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
compilers                 1.5.2                ha770c72_0    conda-forge
contourpy                 1.0.7           py310hdf3cbec_0    conda-forge
cryptography              39.0.2          py310h34c0648_0    conda-forge
cudatoolkit               11.4.2              h7a5bcfd_11    conda-forge
curl                      7.88.1               hdc1c0ab_0    conda-forge
cxx-compiler              1.5.2                hf52228f_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.33         py310heca2aa9_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
debugpy                   1.6.6           py310heca2aa9_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.17.1                   pypi_0    pypi
eigen                     3.4.0                h4bd325d_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.1              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h27087fc_0    conda-forge
fftw                      3.3.10          nompi_hf0379b8_106    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    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                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.39.0          py310h1fa729e_0    conda-forge
fortran-compiler          1.5.2                hdb1a99f_0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
future                    0.18.3                   pypi_0    pypi
gcc                       11.3.0              h02d0930_11    conda-forge
gcc_impl_linux-64         11.3.0              hab1b70f_19    conda-forge
gcc_linux-64              11.3.0              he6f903b_11    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gfortran                  11.3.0              ha859ce3_11    conda-forge
gfortran_impl_linux-64    11.3.0              he34c6f7_19    conda-forge
gfortran_linux-64         11.3.0              h3c55166_11    conda-forge
glew                      2.1.0                h9c3ff4c_2    conda-forge
glib                      2.74.1               h6239696_1    conda-forge
glib-tools                2.74.1               h6239696_1    conda-forge
glm                       0.9.9.4              h924138e_2    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
greenlet                  2.0.2           py310heca2aa9_0    conda-forge
gst-plugins-base          1.22.0               h4243ec0_2    conda-forge
gstreamer                 1.22.0               h25f0c4b_2    conda-forge
gstreamer-orc             0.4.33               h166bdaf_0    conda-forge
gxx                       11.3.0              h02d0930_11    conda-forge
gxx_impl_linux-64         11.3.0              hab1b70f_19    conda-forge
gxx_linux-64              11.3.0              hc203a17_11    conda-forge
harfbuzz                  6.0.0                h8e241bc_0    conda-forge
hdf4                      4.2.15               h9772cbc_5    conda-forge
hdf5                      1.12.2          nompi_h4df4325_101    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.0.0              pyha770c72_0    conda-forge
importlib_metadata        6.0.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.21.3             pyh210e3f2_0    conda-forge
ipython                   8.11.0             pyh41d4057_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.7.3              pyhd8ed1ab_0    conda-forge
jack                      1.9.22               h11f4161_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h166bdaf_2    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            8.0.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.2.0           py310hff52083_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.4.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.1.2              pyhd8ed1ab_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4           py310hbf28c38_1    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lapack                    3.9.0                    netlib    conda-forge
lcms2                     2.15                 hfd0df8a_0    conda-forge
ld_impl_linux-64          2.39                 hcc3a1bd_1    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.0.6                hcb278e6_1    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_8    conda-forge
libbrotlidec              1.0.9                h166bdaf_8    conda-forge
libbrotlienc              1.0.9                h166bdaf_8    conda-forge
libcap                    2.66                 ha37c62d_0    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libclang                  15.0.7          default_had23c3d_1    conda-forge
libclang13                15.0.7          default_h3e3d535_1    conda-forge
libcups                   2.3.3                h36d4200_3    conda-forge
libcurl                   7.88.1               hdc1c0ab_0    conda-forge
libdb                     6.2.32               h9c3ff4c_0    conda-forge
libdeflate                1.17                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h28343ad_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.4.2                h27087fc_0    conda-forge
libgcc-devel_linux-64     11.3.0              h210ce93_19    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgcrypt                 1.10.1               h166bdaf_0    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libglib                   2.74.1               h606061b_1    conda-forge
libglu                    9.0.0             he1b5a44_1001    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libgpg-error              1.46                 h620e276_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             2.1.4                h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libllvm11                 11.1.0               he0ac6c6_5    conda-forge
libllvm15                 15.0.7               hadd5161_1    conda-forge
libnetcdf                 4.8.1           nompi_h261ec11_106    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     15.2                 hb675445_0    conda-forge
libsanitizer              11.3.0              h239ccf8_19    conda-forge
libsndfile                1.2.0                hb75c966_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.40.0               h753d276_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-devel_linux-64  11.3.0              h210ce93_19    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libsystemd0               252                  h2a991cd_0    conda-forge
libtiff                   4.5.0                h6adf6a1_2    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libudev1                  253                  h0b41bf4_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.44.2               h166bdaf_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.3.0                h0b41bf4_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.5.0                h79f4944_1    conda-forge
libxml2                   2.10.3               hca2bb57_3    conda-forge
libxslt                   1.1.37               h873f0b0_0    conda-forge
libzip                    1.9.2                hc929e4a_1    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
llvmlite                  0.39.1          py310h58363a5_1    conda-forge
loos                      4.0.4                    pypi_0    pypi
lxml                      4.9.2           py310hbdc0903_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.1.2           py310h1fa729e_0    conda-forge
matplotlib-base           3.7.1           py310he60537e_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdtraj                    1.9.7           py310h902c554_4    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mmcif-pdbx                2.0.1                    pypi_0    pypi
mmpbsa-py                 16.0                     pypi_0    pypi
mpg123                    1.31.2               hcb278e6_0    conda-forge
mpiplus                   v0.0.1          pyhd8ed1ab_1003    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              8.0.32               ha901b37_0    conda-forge
mysql-libs                8.0.32               hd7da12d_0    conda-forge
nbclassic                 0.5.3              pyhb4ecaf3_3    conda-forge
nbclient                  0.7.2              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.9              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.0           nompi_he1eeb6f_102    conda-forge
netcdf4                   1.6.2           nompi_py310h55e1e36_100    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
nose                      1.3.7                   py_1006    conda-forge
notebook                  6.5.3              pyha770c72_0    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.89                 he45b914_0    conda-forge
numba                     0.56.4          py310ha5257ce_0    conda-forge
numexpr                   2.8.3           py310hf05e7a9_101    conda-forge
numpy                     1.23.5          py310h53a5b5f_0    conda-forge
ocl-icd                   2.3.1                h7f98852_0    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
openblas                  0.3.21          pthreads_h320a7e8_3    conda-forge
openeye-toolkits          2022.2.2                py310_0    openeye
openff-amber-ff-ports     0.0.3              pyh6c4a22f_0    conda-forge
openff-forcefields        2023.02.1          pyh1a96a4e_0    conda-forge
openff-interchange        0.2.3              pyhd8ed1ab_1    conda-forge
openff-interchange-base   0.2.3              pyhd8ed1ab_1    conda-forge
openff-toolkit            0.12.1             pyhd8ed1ab_1    conda-forge
openff-toolkit-base       0.12.1             pyhd8ed1ab_1    conda-forge
openff-units              0.2.0              pyh1a96a4e_0    conda-forge
openff-utilities          0.1.8              pyh1a96a4e_0    conda-forge
openjpeg                  2.5.0                hfec8fc6_2    conda-forge
openmm                    8.0.0           py310h5728c26_0    conda-forge
openmmforcefields         0.11.2             pyhd8ed1ab_1    conda-forge
openmmtools               0.21.5             pyhd8ed1ab_0    conda-forge
openssl                   3.1.0                h0b41bf4_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h86c2bf4_0    conda-forge
packmol-memgen            1.2.3rc0                 pypi_0    pypi
pandas                    1.5.3           py310h9b08913_0    conda-forge
pandoc                    3.1.1                h32600fe_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panedr                    0.7.1              pyhd8ed1ab_0    conda-forge
parmed                    3.4.4           py310heca2aa9_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pbr                       5.11.1             pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pdb2pqr                   3.6.1                    pypi_0    pypi
pdb4amber                 22.0                     pypi_0    pypi
pdbfixer                  1.8.1              pyh6c4a22f_0    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0           py310h023d228_1    conda-forge
pint                      0.20.1             pyhd8ed1ab_0    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.1.1              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
ply                       3.11                       py_1    conda-forge
pmw                       2.0.1           py310hff52083_1007    conda-forge
pmx                       0+untagged.879.gb0b5684          pypi_0    pypi
pooch                     1.7.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
propka                    3.5.0                    pypi_0    pypi
proteinbenchmark          0.0.0+9.g6c1b895.dirty           dev_0    <develop>
psutil                    5.9.4           py310h5764c6d_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulseaudio                16.1                 ha8d29e2_1    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycairo                   1.23.0          py310hb8a676c_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.6          py310h1fa729e_0    conda-forge
pyedr                     0.7.1              pyhd8ed1ab_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pymbar                    3.1.1           py310hde88566_2    conda-forge
pymol-open-source         2.5.0           py310h490904b_6    conda-forge
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.7          py310hab646b1_3    conda-forge
pyqt5-sip                 12.11.0         py310heca2aa9_3    conda-forge
pyrsistent                0.19.3          py310h1fa729e_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.7.0           py310hb60b9b2_3    conda-forge
pytest                    7.2.2              pyhd8ed1ab_0    conda-forge
python                    3.10.9          he550d4f_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
pyyaml                    6.0             py310h5764c6d_5    conda-forge
pyzmq                     25.0.1          py310h059b190_0    conda-forge
qt-main                   5.15.8               h5d23da1_6    conda-forge
rdkit                     2022.09.1       py310h10c98a6_0    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
reportlab                 3.6.12          py310h46e8714_2    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rhash                     1.4.3                h166bdaf_0    conda-forge
sander                    22.0                     pypi_0    pypi
scikit-learn              1.2.2           py310h209a8ca_0    conda-forge
scipy                     1.10.1          py310h8deb116_0    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
seaborn-base              0.12.2             pyhd8ed1ab_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                67.6.0             pyhd8ed1ab_0    conda-forge
sip                       6.7.7           py310heca2aa9_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlalchemy                2.0.6           py310h1fa729e_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.13.5          py310hde88566_2    conda-forge
swig                      4.1.1                h5d7ef5f_0    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tinydb                    4.7.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.2             py310h5764c6d_1    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
unicodedata2              15.0.0          py310h5764c6d_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
validators                0.20.0             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.1              pyha770c72_0    conda-forge
xcb-util                  0.4.0                h516909a_0    conda-forge
xcb-util-image            0.4.0                h166bdaf_0    conda-forge
xcb-util-keysyms          0.4.0                h516909a_0    conda-forge
xcb-util-renderutil       0.3.9                h166bdaf_0    conda-forge
xcb-util-wm               0.4.1                h516909a_0    conda-forge
xkeyboard-config          2.38                 h0b41bf4_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.8.4                h0b41bf4_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xf86vidmodeproto     2.3.1             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge

Additional context
Loading a protein with an NME cap works as intended. Using the python debugger, I can find

> /home/ccavende/anaconda3/envs/openff-proteinbenchmark/lib/python3.10/site-packages/openff/toolkit/utils/openeye_wrapper.py(362)_polymer_openmm_topology_to_oemol()
-> raise UnassignedChemistryInPDBError(
(Pdb) p unassigned_atoms
[]
(Pdb) p unassigned_bonds
[(9, 16)]
(Pdb) p matches
defaultdict(<class 'list'>, {6: ['ALA', 'PEPTIDE_BOND'], 7: ['ALA', 'PEPTIDE_BOND'], 9: ['ALA'], 10: ['ALA'], 8: ['ALA'], 13: ['ALA'], 14: ['ALA'], 15: ['ALA'], 12: ['ALA'], 11: ['ALA'], 4: ['ACE', 'PEPTIDE_BOND'], 5: ['ACE', 'PEPTIDE_BOND'], 1: ['ACE'], 2: ['ACE'], 3: ['ACE'], 0: ['ACE'], 16: ['NH2'], 17: ['NH2'], 18: ['NH2']})

So it looks like the bond between "N" in the NH2 cap and the carbonyl "C" in the previous residue is not recognized.
j-wags added a commit that referenced this issue Apr 26, 2023
@j-wags
fix #1579 and add test
82b8c9d
@j-wags j-wags mentioned this issue Apr 26, 2023
Merged
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j-wags added a commit that referenced this issue Apr 26, 2023
@j-wags @pre-commit-ci
Fix #1579 (#1589)
110ba6f 
* fix #1579 and add test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update file names and release history

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Fix #1579 openforcefield/openff-toolkit
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@chapincavender