Error with linear angle during QC generation within a torsion drive

[eva-not]

Hi, I am trying to get bespoke torsions for the molecule CNC(=O)[C@H](CCC\C=C/CCC[C@H](NC(C)=O)C(=O)NC)NC(C)=O. However, the QC generation step exits with the following message:

3. running the fitting pipeline

[✓] fragmentation successful
[x] qc-generation failed

 [null, null, null, null, null, {"type": "ValueError", "message": "TorsionDrive error at -135:\ngeomeTRIC run_json error:\nTraceback (most recent
 call last):\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/run_json.py\", line 269, in
 geometric_run_json\n    geometric.optimize.Optimize(coords, M, IC, engine, dirname, params, print_info = (ic==0))\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 779, in Optimize\n    return
 optimizer.optimizeGeometry()\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 697, in
 optimizeGeometry\n    self.calcEnergyForce()\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 278, in calcEnergyForce\n
 self.checkStructure()\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 730, in
 checkStructure\n    raise LinearTorsionError(\"A constrained torsion has three consecutive atoms\\n\"\ngeometric.errors.LinearTorsionError: A
 constrained torsion has three consecutive atoms\nforming a nearly linear angle, making the torsion angle poorly defined.\n> Atoms Angle\n> 8-10-12
 179.90\n\n", "traceback": "Traceback (most recent call last):\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/celery/app/trace.py\", line 477, in trace_task\n    R = retval = fun(*args,
 **kwargs)\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/celery/app/trace.py\", line 760, in __protected_call__\n
 return self.run(*args, **kwargs)\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/openff/bespokefit/executor/services/qcgenerator/worker.py\", line 150, in
 compute_torsion_drive\n    return_value = qcengine.compute_procedure(\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/qcengine/compute.py\", line 178, in compute_procedure\n    return
 handle_output_metadata(output_data, metadata, raise_error=raise_error, return_dict=return_dict)\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/qcengine/util.py\", line 183, in handle_output_metadata\n    raise
 ValueError(output_fusion[\"error\"][\"error_message\"])\nValueError: TorsionDrive error at -135:\ngeomeTRIC run_json error:\nTraceback (most
 recent call last):\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/run_json.py\", line 269, in
 geometric_run_json\n    geometric.optimize.Optimize(coords, M, IC, engine, dirname, params, print_info = (ic==0))\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 779, in Optimize\n    return
 optimizer.optimizeGeometry()\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 697, in
 optimizeGeometry\n    self.calcEnergyForce()\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 278, in calcEnergyForce\n
 self.checkStructure()\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 730, in
 checkStructure\n    raise LinearTorsionError(\"A constrained torsion has three consecutive atoms\\n\"\ngeometric.errors.LinearTorsionError: A
 constrained torsion has three consecutive atoms\nforming a nearly linear angle, making the torsion angle poorly defined.\n> Atoms Angle\n> 8-10-12
 179.90\n\n\n"}, null, null, null]

Is there a way to see which atoms these are and which fragment is causing the error? I suspect it's atoms around the C=C double bond, since I ran bespokefit on the same molecule with a single bond instead CNC([C@@H](NC(C)=O)CCCCCCCC[C@@H](C(NC)=O)NC(C)=O)=O and the calculations finished fine (I got a .offxml file).

I also tested bespokefit on a smaller molecule with a C=C double bond O=C(O)/C=C/C(O)=O and I got a similar error:

3. running the fitting pipeline

[✓] fragmentation successful
[x] qc-generation failed

 [{"type": "ValueError", "message": "TorsionDrive error at -75:\ngeomeTRIC run_json error:\nTraceback (most recent call last):\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/run_json.py\", line 269, in geometric_run_json\n
 geometric.optimize.Optimize(coords, M, IC, engine, dirname, params, print_info = (ic==0))\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 779, in Optimize\n    return
 optimizer.optimizeGeometry()\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 697, in
 optimizeGeometry\n    self.calcEnergyForce()\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 278, in calcEnergyForce\n
 self.checkStructure()\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 730, in
 checkStructure\n    raise LinearTorsionError(\"A constrained torsion has three consecutive atoms\\n\"\ngeometric.errors.LinearTorsionError: A
 constrained torsion has three consecutive atoms\nforming a nearly linear angle, making the torsion angle poorly defined.\n> Atoms Angle\n> 5-7-9
 179.94\n\n", "traceback": "Traceback (most recent call last):\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/celery/app/trace.py\", line 477, in trace_task\n    R = retval = fun(*args,
 **kwargs)\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/celery/app/trace.py\", line 760, in __protected_call__\n
 return self.run(*args, **kwargs)\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/openff/bespokefit/executor/services/qcgenerator/worker.py\", line 150, in
 compute_torsion_drive\n    return_value = qcengine.compute_procedure(\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/qcengine/compute.py\", line 178, in compute_procedure\n    return
 handle_output_metadata(output_data, metadata, raise_error=raise_error, return_dict=return_dict)\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/qcengine/util.py\", line 183, in handle_output_metadata\n    raise
 ValueError(output_fusion[\"error\"][\"error_message\"])\nValueError: TorsionDrive error at -75:\ngeomeTRIC run_json error:\nTraceback (most recent
 call last):\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/run_json.py\", line 269, in
 geometric_run_json\n    geometric.optimize.Optimize(coords, M, IC, engine, dirname, params, print_info = (ic==0))\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 779, in Optimize\n    return
 optimizer.optimizeGeometry()\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 697, in
 optimizeGeometry\n    self.calcEnergyForce()\n  File
 \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 278, in calcEnergyForce\n
 self.checkStructure()\n  File \"/home/eva/anaconda3/envs/bespokefit-env/lib/python3.9/site-packages/geometric/optimize.py\", line 730, in
 checkStructure\n    raise LinearTorsionError(\"A constrained torsion has three consecutive atoms\\n\"\ngeometric.errors.LinearTorsionError: A
 constrained torsion has three consecutive atoms\nforming a nearly linear angle, making the torsion angle poorly defined.\n> Atoms Angle\n> 5-7-9
 179.94\n\n\n"}, null]

Bespokefit is ran via the CLI:

BEFLOW_OPTIMIZER_KEEP_FILES=True openff-bespoke executor run --smiles "CNC(=O)[C@H](CCC\C=C/CCC[C@H](NC(C)=O)C(=O)NC)NC(C)=O" --workflow-file "factory.json" --output-force-field "ff.offxml" --n-fragmenter-workers 6 --n-qc-compute-workers 12 --qc-compute-n-cores 4 --n-optimizer-workers 6 --directory ./fitting

The workflow file is: factory.json

Any help with this would be greatly appreciated!

Software versions

• Which operating system and version are you using? Ubuntu 20.04 LTS
• How did you install BespokeFit? mamba install -c conda-forge openff-bespokefit
• Are you using Apple Silicon? If so, are you running BespokeFit in Rosetta or directly? No
• What is the output of running conda list?

Output of conda list

Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge

_openmp_mutex             4.5                       2_gnu    conda-forge

amberlite                 16.0                     pypi_0    pypi

ambertools                20.9                     pypi_0    pypi

ambit                     0.6              py39h53dec33_2    psi4

amqp                      5.1.1              pyhd8ed1ab_0    conda-forge

anyio                     3.7.1              pyhd8ed1ab_0    conda-forge

argcomplete               3.1.2              pyhd8ed1ab_0    conda-forge

argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge

argon2-cffi-bindings      21.2.0           py39hd1e30aa_4    conda-forge

arpack                    3.7.0                hc6cf775_2    conda-forge

arrow                     1.3.0              pyhd8ed1ab_0    conda-forge

asttokens                 2.4.0              pyhd8ed1ab_0    conda-forge

astunparse                1.6.3              pyhd8ed1ab_0    conda-forge

async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge

async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge

attrs                     23.1.0             pyh71513ae_1    conda-forge

aws-c-auth                0.7.4                hc8144f4_1    conda-forge

aws-c-cal                 0.6.2                h09139f6_2    conda-forge

aws-c-common              0.9.3                hd590300_0    conda-forge

aws-c-compression         0.2.17               h184a658_3    conda-forge

aws-c-event-stream        0.3.2                hd6ebb48_1    conda-forge

aws-c-http                0.7.13               hc690213_1    conda-forge

aws-c-io                  0.13.32              h63140e9_5    conda-forge

aws-c-mqtt                0.9.6                h32970c0_2    conda-forge

aws-c-s3                  0.3.17               hb5e3142_3    conda-forge

aws-c-sdkutils            0.1.12               h184a658_2    conda-forge

aws-checksums             0.1.17               h184a658_2    conda-forge

aws-crt-cpp               0.23.1               h94c364a_5    conda-forge

aws-sdk-cpp               1.11.156             h6600424_3    conda-forge

babel                     2.12.1             pyhd8ed1ab_1    conda-forge

backcall                  0.2.0              pyh9f0ad1d_0    conda-forge

backports                 1.0                pyhd8ed1ab_3    conda-forge

backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge

backports.zoneinfo        0.2.1            py39hf3d152e_8    conda-forge

basis_set_exchange        0.9.1              pyhd8ed1ab_0    conda-forge

beautifulsoup4            4.12.2             pyha770c72_0    conda-forge

billiard                  4.1.0            py39hd1e30aa_1    conda-forge

blas                      1.0                         mkl    conda-forge

bleach                    6.0.0              pyhd8ed1ab_0    conda-forge

blosc                     1.21.5               h0f2a231_0    conda-forge

boltons                   23.0.0             pyhd8ed1ab_0    conda-forge

boost                     1.74.0           py39h5472131_5    conda-forge

boost-cpp                 1.74.0               h75c5d50_8    conda-forge

brotli                    1.1.0                hd590300_1    conda-forge

brotli-bin                1.1.0                hd590300_1    conda-forge

brotli-python             1.1.0            py39h3d6467e_1    conda-forge

bzip2                     1.0.8                h7f98852_4    conda-forge

c-ares                    1.19.1               hd590300_0    conda-forge

ca-certificates           2023.7.22            hbcca054_0    conda-forge

cached-property           1.5.2                hd8ed1ab_1    conda-forge

cached_property           1.5.2              pyha770c72_1    conda-forge

cachetools                5.3.1              pyhd8ed1ab_0    conda-forge

cairo                     1.16.0            ha61ee94_1014    conda-forge

celery                    5.3.4              pyhd8ed1ab_1    conda-forge

certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge

cffi                      1.16.0           py39h7a31438_0    conda-forge

charset-normalizer        3.3.0              pyhd8ed1ab_0    conda-forge

chemper                   1.0.1              pyhd8ed1ab_0    conda-forge

chemps2                   1.8.11               hbe8a562_0    psi4

click                     8.1.7           unix_pyh707e725_0    conda-forge

click-didyoumean          0.3.0              pyhd8ed1ab_0    conda-forge

click-option-group        0.5.6              pyhd8ed1ab_0    conda-forge

click-plugins             1.1.1                      py_0    conda-forge

click-repl                0.3.0              pyhd8ed1ab_0    conda-forge

colorama                  0.4.6              pyhd8ed1ab_0    conda-forge

comm                      0.1.4              pyhd8ed1ab_0    conda-forge

conda                     23.7.4           py39hf3d152e_0    conda-forge

conda-package-handling    2.2.0              pyh38be061_0    conda-forge

conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge

contourpy                 1.1.1            py39h7633fee_1    conda-forge

cryptography              41.0.4           py39hd4f0224_0    conda-forge

cuda-cudart               12.0.107             h59595ed_6    conda-forge

cuda-cudart_linux-64      12.0.107             h59595ed_6    conda-forge

cuda-nvrtc                12.0.76              h59595ed_1    conda-forge

cuda-version              12.0                 hffde075_2    conda-forge

curl                      8.3.0                hca28451_0    conda-forge

cycler                    0.12.0             pyhd8ed1ab_0    conda-forge

cython                    3.0.3            py39h3d6467e_0    conda-forge

debugpy                   1.8.0            py39h3d6467e_1    conda-forge

decorator                 5.1.1              pyhd8ed1ab_0    conda-forge

defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge

dftd3                     3.2.1                h84218bc_2    psi4

dkh                       1.2                  h173d85e_2    psi4

entrypoints               0.4                pyhd8ed1ab_0    conda-forge

exceptiongroup            1.1.3              pyhd8ed1ab_0    conda-forge

executing                 1.2.0              pyhd8ed1ab_0    conda-forge

expat                     2.5.0                hcb278e6_1    conda-forge

fastapi                   0.86.0             pyhd8ed1ab_0    conda-forge

fftw                      3.3.8           nompi_hfc0cae8_1114    conda-forge

fmt                       10.1.1               h00ab1b0_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                 4.43.1           py39hd1e30aa_0    conda-forge

forcebalance              1.9.5            py39h0354152_0    conda-forge

fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge

freetype                  2.12.1               h267a509_2    conda-forge

freetype-py               2.3.0              pyhd8ed1ab_0    conda-forge

future                    0.18.3             pyhd8ed1ab_0    conda-forge

gau2grid                  2.0.7                hd18ef5c_0    psi4

gcp                       2.0.2                he991be0_2    psi4

gdma                      2.2.6                h0e1e685_6    psi4

geometric                 1.0                pyhd8ed1ab_1    conda-forge

gettext                   0.21.1               h27087fc_0    conda-forge

gflags                    2.2.2             he1b5a44_1004    conda-forge

glog                      0.6.0                h6f12383_0    conda-forge

greenlet                  3.0.0            py39h3d6467e_1    conda-forge

h11                       0.14.0             pyhd8ed1ab_0    conda-forge

h2                        4.1.0              pyhd8ed1ab_0    conda-forge

h5py                      3.7.0            py39h737f45e_0

hdf4                      4.2.15               h9772cbc_5    conda-forge

hdf5                      1.10.6          nompi_h3c11f04_101    conda-forge

hpack                     4.0.0              pyh9f0ad1d_0    conda-forge

httpcore                  0.18.0             pyhd8ed1ab_0    conda-forge

httpx                     0.25.0             pyhd8ed1ab_0    conda-forge

hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge

icu                       70.1                 h27087fc_0    conda-forge

idna                      3.4                pyhd8ed1ab_0    conda-forge

importlib-metadata        6.8.0              pyha770c72_0    conda-forge

importlib-resources       6.1.0              pyhd8ed1ab_0    conda-forge

importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge

importlib_resources       6.1.0              pyhd8ed1ab_0    conda-forge

iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge

intel-openmp              2021.4.0          h06a4308_3561

ipykernel                 6.25.2             pyh2140261_0    conda-forge

ipython                   8.16.1             pyh0d859eb_0    conda-forge

ipython_genutils          0.2.0                      py_1    conda-forge

ipywidgets                7.8.0              pyhd8ed1ab_0    conda-forge

isoduration               20.11.0            pyhd8ed1ab_0    conda-forge

jedi                      0.19.1             pyhd8ed1ab_0    conda-forge

jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge

jpeg                      9e                   h0b41bf4_3    conda-forge

json5                     0.9.14             pyhd8ed1ab_0    conda-forge

jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge

jsonpointer               2.4              py39hf3d152e_3    conda-forge

jsonschema                4.19.1             pyhd8ed1ab_0    conda-forge

jsonschema-specifications 2023.7.1           pyhd8ed1ab_0    conda-forge

jsonschema-with-format-nongpl 4.19.1             pyhd8ed1ab_0    conda-forge

jupyter-lsp               2.2.0              pyhd8ed1ab_0    conda-forge

jupyter_client            8.3.1              pyhd8ed1ab_0    conda-forge

jupyter_core              5.3.2            py39hf3d152e_0    conda-forge

jupyter_events            0.7.0              pyhd8ed1ab_2    conda-forge

jupyter_server            2.7.3              pyhd8ed1ab_1    conda-forge

jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge

jupyterlab                4.0.6              pyhd8ed1ab_0    conda-forge

jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge

jupyterlab_server         2.25.0             pyhd8ed1ab_0    conda-forge

jupyterlab_widgets        1.1.7              pyhd8ed1ab_0    conda-forge

keyutils                  1.6.1                h166bdaf_0    conda-forge

kiwisolver                1.4.5            py39h7633fee_1    conda-forge

kombu                     5.3.2            py39hf3d152e_1    conda-forge

krb5                      1.21.2               h659d440_0    conda-forge

lcms2                     2.15                 hfd0df8a_0    conda-forge

ld_impl_linux-64          2.40                 h41732ed_0    conda-forge

lerc                      4.0.0                h27087fc_0    conda-forge

libabseil                 20230802.1      cxx17_h59595ed_0    conda-forge

libarchive                3.6.2                h3d51595_0    conda-forge

libarrow                  13.0.0           hc3189b8_6_cpu    conda-forge

libblas                   3.9.0            12_linux64_mkl    conda-forge

libbrotlicommon           1.1.0                hd590300_1    conda-forge

libbrotlidec              1.1.0                hd590300_1    conda-forge

libbrotlienc              1.1.0                hd590300_1    conda-forge

libcblas                  3.9.0            12_linux64_mkl    conda-forge

libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge

libcufft                  11.0.0.21            hcb278e6_1    conda-forge

libcurl                   8.3.0                hca28451_0    conda-forge

libdeflate                1.17                 h0b41bf4_0    conda-forge

libecpint                 1.0.7                hfebba4c_0    psi4

libedit                   3.1.20191231         he28a2e2_2    conda-forge

libev                     4.33                 h516909a_1    conda-forge

libevent                  2.1.12               hf998b51_1    conda-forge

libexpat                  2.5.0                hcb278e6_1    conda-forge

libffi                    3.4.2                h7f98852_5    conda-forge

libgcc-ng                 13.2.0               h807b86a_2    conda-forge

libgfortran-ng            7.5.0               h14aa051_20    conda-forge

libgfortran4              7.5.0               h14aa051_20    conda-forge

libglib                   2.78.0               hebfc3b9_0    conda-forge

libgomp                   13.2.0               h807b86a_2    conda-forge

libgoogle-cloud           2.12.0               h8d7e28b_2    conda-forge

libgrpc                   1.57.0               ha4d0f93_1    conda-forge

libiconv                  1.17                 h166bdaf_0    conda-forge

libint2                   2.7.1               h2fe1556_15    psi4

liblapack                 3.9.0            12_linux64_mkl    conda-forge

libmamba                  1.5.1                h744094f_0    conda-forge

libmambapy                1.5.1            py39h10defb6_0    conda-forge

libnetcdf                 4.7.4           nompi_h56d31a8_107    conda-forge

libnghttp2                1.52.0               h61bc06f_0    conda-forge

libnsl                    2.0.0                hd590300_1    conda-forge

libnuma                   2.0.16               h0b41bf4_1    conda-forge

libpng                    1.6.39               h753d276_0    conda-forge

libprotobuf               4.23.4               hf27288f_6    conda-forge

libsodium                 1.0.18               h36c2ea0_1    conda-forge

libsolv                   0.7.25               hfc55251_0    conda-forge

libsqlite                 3.43.0               h2797004_0    conda-forge

libssh2                   1.11.0               h0841786_0    conda-forge

libstdcxx-ng              13.2.0               h7e041cc_2    conda-forge

libthrift                 0.19.0               hb90f79a_1    conda-forge

libtiff                   4.5.0                h6adf6a1_2    conda-forge

libutf8proc               2.8.0                h166bdaf_0    conda-forge

libuuid                   2.38.1               h0b41bf4_0    conda-forge

libwebp-base              1.3.2                hd590300_0    conda-forge

libxc                     5.2.3                hfebba4c_0    psi4

libxcb                    1.13              h7f98852_1004    conda-forge

libxml2                   2.10.3               hca2bb57_4    conda-forge

libxslt                   1.1.37               h873f0b0_0    conda-forge

libzlib                   1.2.13               hd590300_5    conda-forge

lxml                      4.9.2            py39h14694de_0    conda-forge

lz4-c                     1.9.4                hcb278e6_0    conda-forge

lzo                       2.10              h516909a_1000    conda-forge

mamba                     1.5.1            py39hc5d2bb1_0    conda-forge

markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge

markupsafe                2.1.3            py39hd1e30aa_1    conda-forge

matplotlib-base           3.8.0            py39he9076e7_1    conda-forge

matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge

mda-xdrlib                0.2.0              pyhd8ed1ab_0    conda-forge

mdtraj                    1.9.9            py39h031bd0f_0    conda-forge

mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge

mistune                   3.0.1              pyhd8ed1ab_0    conda-forge

mkl                       2021.4.0           h06a4308_640

mkl-service               2.4.0            py39h7e14d7c_0    conda-forge

mmpbsa-py                 16.0                     pypi_0    pypi

mock                      5.1.0              pyhd8ed1ab_0    conda-forge

msgpack-python            1.0.6            py39h7633fee_0    conda-forge

munkres                   1.1.4              pyh9f0ad1d_0    conda-forge

nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge

nbconvert-core            7.9.2              pyhd8ed1ab_0    conda-forge

nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge

ncurses                   6.4                  hcb278e6_0    conda-forge

nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge

netcdf-fortran            4.5.3           nompi_hfef6a68_101    conda-forge

networkx                  3.1                pyhd8ed1ab_0    conda-forge

nglview                   3.0.8              pyh1da8cd4_0    conda-forge

notebook                  7.0.4              pyhd8ed1ab_0    conda-forge

notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge

numexpr                   2.7.3            py39hde0f152_1    conda-forge

numpy                     1.25.2           py39h6183b62_0    conda-forge

ocl-icd                   2.3.1                h7f98852_0    conda-forge

ocl-icd-system            1.0.0                         1    conda-forge

openff-amber-ff-ports     0.0.3              pyh6c4a22f_0    conda-forge

openff-bespokefit         0.2.2              pyhd8ed1ab_5    conda-forge

openff-forcefields        2023.08.0          pyh1a96a4e_0    conda-forge

openff-fragmenter-base    0.2.0              pyhd8ed1ab_0    conda-forge

openff-interchange        0.3.1              pyhd8ed1ab_1    conda-forge

openff-interchange-base   0.3.1              pyhd8ed1ab_1    conda-forge

openff-models             0.1.0              pyh1a96a4e_1    conda-forge

openff-qcsubmit           0.5.0              pyhd8ed1ab_0    conda-forge

openff-toolkit            0.12.1             pyhd8ed1ab_0    conda-forge

openff-toolkit-base       0.12.1             pyhd8ed1ab_0    conda-forge

openff-units              0.2.1              pyh1a96a4e_0    conda-forge

openff-utilities          0.1.10             pyhd8ed1ab_0    conda-forge

openjpeg                  2.5.0                hfec8fc6_2    conda-forge

openmm                    8.0.0            py39h5d72b6b_3    conda-forge

openssl                   3.1.3                hd590300_0    conda-forge

optking                   0.2.1              pyhbc12335_1    psi4

orc                       1.9.0                h52d3b3c_2    conda-forge

overrides                 7.4.0              pyhd8ed1ab_0    conda-forge

packaging                 23.2               pyhd8ed1ab_0    conda-forge

packmol-memgen            1.1.0rc0                 pypi_0    pypi

pandas                    1.4.4            py39h1832856_0    conda-forge

pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge

panedr                    0.7.2              pyhd8ed1ab_0    conda-forge

parmed                    at20RC5+54.g5702a232fe.dirty          pypi_0    pypi

parso                     0.8.3              pyhd8ed1ab_0    conda-forge

pbr                       5.11.1             pyhd8ed1ab_0    conda-forge

pcmsolver                 1.2.1.1          py39h92d4acf_3    psi4

pcre2                     10.40                hc3806b6_0    conda-forge

pdb4amber                 1.7.dev0                 pypi_0    pypi

perl                      5.32.1          4_hd590300_perl5    conda-forge

pexpect                   4.8.0              pyh1a96a4e_2    conda-forge

pickleshare               0.7.5                   py_1003    conda-forge

pillow                    9.4.0            py39h2320bf1_1    conda-forge

pint                      0.21               pyhd8ed1ab_0    conda-forge

pip                       23.2.1             pyhd8ed1ab_0    conda-forge

pixman                    0.42.2               h59595ed_0    conda-forge

pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge

platformdirs              3.11.0             pyhd8ed1ab_0    conda-forge

plotly                    5.17.0             pyhd8ed1ab_0    conda-forge

pluggy                    1.3.0              pyhd8ed1ab_0    conda-forge

prometheus_client         0.17.1             pyhd8ed1ab_0    conda-forge

prompt-toolkit            3.0.39             pyha770c72_0    conda-forge

prompt_toolkit            3.0.39               hd8ed1ab_0    conda-forge

psi4                      1.7+6ce35a5      py39hb8090b1_1    psi4

psutil                    5.9.5            py39hd1e30aa_1    conda-forge

pthread-stubs             0.4               h36c2ea0_1001    conda-forge

ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge

pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge

py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge

pyarrow                   13.0.0          py39h6925388_6_cpu    conda-forge

pybind11-abi              4                    hd8ed1ab_3    conda-forge

pycairo                   1.25.0           py39hc92de75_1    conda-forge

pycosat                   0.6.6            py39hd1e30aa_0    conda-forge

pycparser                 2.21               pyhd8ed1ab_0    conda-forge

pydantic                  1.10.13          py39hd1e30aa_0    conda-forge

pyedr                     0.7.2              pyhd8ed1ab_0    conda-forge

pygments                  2.16.1             pyhd8ed1ab_0    conda-forge

pymbar                    3.1.1            py39h2ae25f5_2    conda-forge

pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge

pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge

pysocks                   1.7.1              pyha2e5f31_6    conda-forge

pytables                  3.6.1            py39hf6dc253_3    conda-forge

pytest                    7.4.2              pyhd8ed1ab_0    conda-forge

python                    3.9.18          h0755675_0_cpython    conda-forge

python-constraint         1.4.0                      py_0    conda-forge

python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge

python-fastjsonschema     2.18.1             pyhd8ed1ab_0    conda-forge

python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge

python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge

python_abi                3.9                      4_cp39    conda-forge

pytraj                    2.0.5                    pypi_0    pypi

pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge

pyyaml                    6.0.1            py39hd1e30aa_1    conda-forge

pyzmq                     25.1.1           py39hb257651_1    conda-forge

qcelemental               0.25.1             pyhd8ed1ab_1    psi4

qcengine                  0.26.0             pyhd8ed1ab_0    psi4

qcportal                  0.15.8             pyhd8ed1ab_1    conda-forge

rdkit                     2022.09.1        py39h79face8_0    conda-forge

rdma-core                 28.9                 h59595ed_1    conda-forge

re2                       2023.03.02           h8c504da_0    conda-forge

readline                  8.2                  h8228510_1    conda-forge

redis-py                  5.0.1              pyhd8ed1ab_0    conda-forge

redis-server              7.2.1                h06160fa_0    conda-forge

referencing               0.30.2             pyhd8ed1ab_0    conda-forge

regex                     2023.10.3        py39hd1e30aa_0    conda-forge

reportlab                 4.0.4            py39hd1e30aa_0    conda-forge

reproc                    14.2.4.post0         hd590300_0    conda-forge

reproc-cpp                14.2.4.post0         h59595ed_0    conda-forge

requests                  2.31.0             pyhd8ed1ab_0    conda-forge

rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge

rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge

rich                      13.6.0             pyhd8ed1ab_0    conda-forge

rlpycairo                 0.2.0              pyhd8ed1ab_0    conda-forge

rpds-py                   0.10.4           py39h9fdd4d6_0    conda-forge

ruamel.yaml               0.17.35          py39hd1e30aa_0    conda-forge

ruamel.yaml.clib          0.2.7            py39hd1e30aa_2    conda-forge

s2n                       1.3.52               h06160fa_0    conda-forge

sander                    16.0                     pypi_0    pypi

scipy                     1.5.3            py39hf3f25e7_0    conda-forge

send2trash                1.8.2              pyh41d4057_0    conda-forge

setuptools                68.2.2             pyhd8ed1ab_0    conda-forge

simint                    0.7                  h642920c_1    psi4

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                 2.5                pyhd8ed1ab_1    conda-forge

sqlalchemy                2.0.21           py39hd1e30aa_1    conda-forge

stack_data                0.6.2              pyhd8ed1ab_0    conda-forge

starlette                 0.20.4             pyhd8ed1ab_1    conda-forge

tenacity                  8.2.3              pyhd8ed1ab_0    conda-forge

terminado                 0.17.1             pyh41d4057_0    conda-forge

tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge

tk                        8.6.13               h2797004_0    conda-forge

tomli                     2.0.1              pyhd8ed1ab_0    conda-forge

toolz                     0.12.0             pyhd8ed1ab_0    conda-forge

tornado                   6.3.3            py39hd1e30aa_1    conda-forge

torsiondrive              1.1.0              pyhd8ed1ab_0    conda-forge

tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge

traitlets                 5.11.2             pyhd8ed1ab_0    conda-forge

types-python-dateutil     2.8.19.14          pyhd8ed1ab_0    conda-forge

typing-extensions         4.8.0                hd8ed1ab_0    conda-forge

typing_extensions         4.8.0              pyha770c72_0    conda-forge

typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge

tzdata                    2023c                h71feb2d_0    conda-forge

ucx                       1.15.0               h195a15c_0    conda-forge

unicodedata2              15.1.0           py39hd1e30aa_0    conda-forge

unidecode                 1.3.7              pyhd8ed1ab_0    conda-forge

uri-template              1.3.0              pyhd8ed1ab_0    conda-forge

urllib3                   2.0.6              pyhd8ed1ab_0    conda-forge

uvicorn                   0.23.2           py39hf3d152e_1    conda-forge

vine                      5.0.0              pyhd8ed1ab_1    conda-forge

wcwidth                   0.2.8              pyhd8ed1ab_0    conda-forge

webcolors                 1.13               pyhd8ed1ab_0    conda-forge

webencodings              0.5.1              pyhd8ed1ab_2    conda-forge

websocket-client          1.6.3              pyhd8ed1ab_0    conda-forge

wheel                     0.41.2             pyhd8ed1ab_0    conda-forge

widgetsnbextension        3.6.6              pyhd8ed1ab_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               1.0.11               hd590300_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                1.3.0                hd590300_0    conda-forge

xorg-renderproto          0.11.1            h7f98852_1002    conda-forge

xorg-xextproto            7.3.0             h0b41bf4_1003    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

yaml-cpp                  0.7.0                h59595ed_3    conda-forge

zeromq                    4.3.4                h9c3ff4c_1    conda-forge

zipp                      3.17.0             pyhd8ed1ab_0    conda-forge

zlib                      1.2.13               hd590300_5    conda-forge

zstandard                 0.21.0           py39h6e5214e_1    conda-forge

zstd                      1.5.5                hfc55251_0    conda-forge

[mattwthompson]

Hi, sorry for the delay. This looks pretty tricky - thanks for all the info, it really helps track stuff down.

My first idea is to capture errors in the function call to QCEngine and re-raise the error with extra info about the fragment. That wouldn't fix it, but it would provide more information about the specific fragment that's causing the failure. Since geomeTRIC is already providing a decent amount of information about the failure, I don't think it's reasonable to ask it to provide more info ("and here is the mapped SMILES of the full molecule:" etc.)

A more robust solution would probably be #295; I figure you shouldn't normally have linear triplets around a double bond, so this is just a funky chemistry forced by driving the torsion, so skipping that one particular structure is justified.

We recently released a new version (0.2.3) with a couple of improvements related to torsion drives (parallelization #277 and re-starting failed jobs #279) but if I understand the issue correctly, neither of these really address the root cause. It still might be worth a shot.

[eva-not]

Hi, thank you very much for the reply. Unfortunately I can't skip this particular structure as it's one of the few I would like to optimise. I will probably have to resort to manual torsion scans.