OpenFF Industry Benchmark Season 1 - MM v1.1 #218

dotsdl · 2021-07-30T14:51:27Z

MM optimizations based on completed QM optimization final geometries from the OpenFF Industry Benchmark Season 1 v1.1 dataset.

New Submission Checklist

Created a new folder in the submissions directory containing the dataset
Added README.md describing the dataset see here for examples
All files used to produce the dataset are included with a description
Dataset follows the QCSubmit schema defined for Datasets, OptimizationDatasets and TorsionDriveDatasets
Dataset filename matches pattern dataset*.json; may feature a compression extension, such as .bz2
A PDF depicting the molecules is attached, in the case of torsiondrives this should include the highlighting of the central bond, this can be done automatically using qcsubmit.
QCSubmit validation passed
Made a new dataset entry in the mapping table in repository README.md
Ready to submit!

dotsdl · 2021-07-30T14:54:19Z

@jthorton please review when you have a chance. @bennybp and I managed to get the MM specs on the original submission unstuck, so getting this merged is somewhat less urgent. I will be officially back online Wednesday, Tuesday earliest, to address any comments.

Thank you!

openff-dangerbot · 2021-07-30T15:09:21Z

QCSubmit Validation Report

	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2
Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
Elements	N ,F ,Cl ,O ,Br ,S ,H ,C ,P
Valid Cmiles	✔️
Connected Dihedrals	✔️
No Linear Torsions	✔️
No Molecular Complexes	✔️
Valid Constraints	✔️
Complete Metatdata	✔️
Valid SCF Properties	✔️

QC Specification Report

	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/smirnoff99Frosst-1.1.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.0.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.1.1	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.2.1	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.3.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/gaff-2.11
Specification Name	smirnoff99Frosst-1.1.0	openff-1.0.0	openff-1.1.1	openff-1.2.1	openff-1.3.0	gaff-2.11
Method	smirnoff99frosst-1.1.0	openff-1.0.0	openff-1.1.1	openff-1.2.1	openff-1.3.0	gaff-2.11
Basis	smirnoff	smirnoff	smirnoff	smirnoff	smirnoff	antechamber
Wavefunction Protocol	none	none	none	none	none	none
Implicit Solvent
Keywords	{}	{}	{}	{}	{}	{}
Validated	✔️	✔️	✔️	✔️	✔️	✔️
Full Basis Coverage	✔️	✔️	✔️	✔️	✔️	✔️

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.9.2
basis_set_exchange	v0.8.13
qcelemental	v0.21.0
rdkit	2021.03.4

pavankum · 2021-08-08T21:07:38Z

@dotsdl I don't have the benchmark env set up so I am not sure how the dataset was generated using
!openff-benchmark optimize create-submittable -o "dataset-mm.json.bz2" --dataset-name "OpenFF Industry Benchmark Season 1 - MM v1.1" --season "1:2" data/results-qm/default/.

Some warnings during the above step seem to be dangerous like,

Warning: molecule is tagged as 3D, but all Z coords are zero,
WARNING: Charges were rearranged,
WARNING: Proton(s) added/removed,
but if I read the molecules in the final dataset.json file they look fine, it's a bit confusing.

Another thing I observed is that all the molecules in the json have a BRI tag which represents only one company, is it the intent or others might be missing? I think @jthorton would be in a better place to review this PR. If his plate his full I can take another look.

dotsdl · 2021-08-09T23:25:43Z

@dotsdl I don't have the benchmark env set up so I am not sure how the dataset was generated using
!openff-benchmark optimize create-submittable -o "dataset-mm.json.bz2" --dataset-name "OpenFF Industry Benchmark Season 1 - MM v1.1" --season "1:2" data/results-qm/default/.

Ah, thank you! I've now added an env file that builds the environment I used. The inputs to create-submittable are the outputs from the export, which is SDF files giving the final geometry of all QM optimizations from "OpenFF Industry Benchmark Season 1 v1.1".

Some warnings during the above step seem to be dangerous like,
* `Warning: molecule is tagged as 3D, but all Z coords are zero`,

In working with the partners, I think we identified these warnings as all being molecules that are flat/2D, even though the SDFs themselves are all 3D. Would have to do a more thorough analysis to determine if this is true for all cases, however. @j-wags is this consistent with your memory?

* `WARNING: Charges were rearranged`,

* `WARNING: Proton(s) added/removed`,
  but if I read the molecules in the final dataset.json file they look fine, it's a bit confusing.

We encounter these a lot with taking the QM mols and running them through RDKIT. @j-wags I think we had concluded in the benchmark work with partners that these weren't too concerning? I don't recall our conclusions off-hand, however.

Another thing I observed is that all the molecules in the json have a BRI tag which represents only one company, is it the intent or others might be missing? I think @jthorton would be in a better place to review this PR. If his plate his full I can take another look.

I'm seeing the following prefixes among the keys under the top-level 'dataset' key:

{'BRI', 'GNT', 'JNS', 'MRK', 'RCH', 'WCS', 'XTP'}

@pavankum where are you only seeing BRI represented?

j-wags · 2021-08-09T23:32:33Z

In working with the partners, I think we identified these warnings as all being molecules that are flat/2D, even though the SDFs themselves are all 3D. Would have to do a more thorough analysis to determine if this is true for all cases, however. @j-wags is this consistent with your memory?

Yes, the "2D" warnings are just fine. Some molecules are planar, and some conformer generation methods have a convention of laying them flat with all z=0, which can make RDKit emit this warning on subsequent reads of that file.

WARNING: Proton(s) added/removed,
but if I read the molecules in the final dataset.json file they look fine, it's a bit confusing.

We encounter these a lot with taking the QM mols and running them through RDKIT. @j-wags I think we had concluded in the benchmark work with partners that these weren't too concerning? I don't recall our conclusions off-hand, however.

Yup, these are fine too. IIRC, we tracked this down to the InChI toolkit populating metadata for the submission and doing weird InChI stuff to the protonation in the process. The molecule with protons getting added/removed is a copy that never comes back into the workflow, so this doesn't affect the underlying molecule.

openff-dangerbot · 2021-08-09T23:37:40Z

QCSubmit Validation Report

	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2
Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
Elements	N ,F ,Cl ,O ,Br ,S ,H ,C ,P
Valid Cmiles	✔️
Connected Dihedrals	✔️
No Linear Torsions	✔️
No Molecular Complexes	✔️
Valid Constraints	✔️
Complete Metatdata	✔️
Valid SCF Properties	✔️

QC Specification Report

	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/smirnoff99Frosst-1.1.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.0.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.1.1	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.2.1	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.3.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/gaff-2.11
Specification Name	smirnoff99Frosst-1.1.0	openff-1.0.0	openff-1.1.1	openff-1.2.1	openff-1.3.0	gaff-2.11
Method	smirnoff99frosst-1.1.0	openff-1.0.0	openff-1.1.1	openff-1.2.1	openff-1.3.0	gaff-2.11
Basis	smirnoff	smirnoff	smirnoff	smirnoff	smirnoff	antechamber
Wavefunction Protocol	none	none	none	none	none	none
Implicit Solvent
Keywords	{}	{}	{}	{}	{}	{}
Validated	✔️	✔️	✔️	✔️	✔️	✔️
Full Basis Coverage	✔️	✔️	✔️	✔️	✔️	✔️

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.21.0
rdkit	2021.03.4

pavankum · 2021-08-10T01:49:35Z

@dotsdl Awesome! Thank you very much for the clarifications.

where are you only seeing BRI represented?

That was my mistake, sorry about that. I printed out the dataset and didn't notice that it was truncated after a few records with three tiny extension dots. I printed the dataset keys and all the tags you mentioned are present, and the total no. of entries is 71655.

One last minor block for me, I created the env and tried openff-benchmark optimize export , but it is throwing the following error for me,

Traceback (most recent call last):
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/bin/openff-benchmark", line 5, in <module>
    from openff.benchmark.cli import cli
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/lib/python3.7/site-packages/openff/benchmark/cli.py", line 492, in <module>
    @click.option('--output-directory', default='5-compare_forcefields', required=True)
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/lib/python3.7/site-packages/click/decorators.py", line 247, in decorator
    _param_memo(f, OptionClass(param_decls, **option_attrs))
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/lib/python3.7/site-packages/click/core.py", line 2482, in __init__
    super().__init__(param_decls, type=type, multiple=multiple, **attrs)
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/lib/python3.7/site-packages/click/core.py", line 2110, in __init__
    ) from None
ValueError: 'default' must be a list when 'multiple' is true.

When I replace multiple=True in cli.py with multiple=False I was able to run the command and generate SDF files so this is a non-issue for me, I don't want to delay further and pushing this submission through. You can merge this as it is.

pavankum

Thank you for building this dataset!!

…ission

dotsdl · 2021-08-10T07:40:10Z

One last minor block for me, I created the env and tried openff-benchmark optimize export , but it is throwing the following error for me,

Traceback (most recent call last):
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/bin/openff-benchmark", line 5, in <module>
    from openff.benchmark.cli import cli
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/lib/python3.7/site-packages/openff/benchmark/cli.py", line 492, in <module>
    @click.option('--output-directory', default='5-compare_forcefields', required=True)
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/lib/python3.7/site-packages/click/decorators.py", line 247, in decorator
    _param_memo(f, OptionClass(param_decls, **option_attrs))
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/lib/python3.7/site-packages/click/core.py", line 2482, in __init__
    super().__init__(param_decls, type=type, multiple=multiple, **attrs)
  File "/home/maverick/anaconda3/envs/openff-benchmark-optimization-export-multi/lib/python3.7/site-packages/click/core.py", line 2110, in __init__
    ) from None
ValueError: 'default' must be a list when 'multiple' is true.

When I replace multiple=True in cli.py with multiple=False I was able to run the command and generate SDF files so this is a non-issue for me, I don't want to delay further and pushing this submission through. You can merge this as it is.

Ah, I forgot we pinned click=7.1.2 in the prod envs to keep it from drifting forward on us. The issue you identified and fixed is also fixed in master, I think, but we pinned click anyway to avoid additional surprises coming down for our prod envs. I've pinned this in the env file in this submission as well to avoid the issue fore reproducibility.

dotsdl · 2021-08-10T07:41:37Z

Thanks @pavankum! Will merge this with fresh eyes in the morning. Much appreciated for the thorough review!

openff-dangerbot · 2021-08-10T07:54:59Z

QCSubmit Validation Report

	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2
Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
Elements	N ,F ,Cl ,O ,Br ,S ,H ,C ,P
Valid Cmiles	✔️
Connected Dihedrals	✔️
No Linear Torsions	✔️
No Molecular Complexes	✔️
Valid Constraints	✔️
Complete Metatdata	✔️
Valid SCF Properties	✔️

QC Specification Report

	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/smirnoff99Frosst-1.1.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.0.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.1.1	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.2.1	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.3.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/gaff-2.11
Specification Name	smirnoff99Frosst-1.1.0	openff-1.0.0	openff-1.1.1	openff-1.2.1	openff-1.3.0	gaff-2.11
Method	smirnoff99frosst-1.1.0	openff-1.0.0	openff-1.1.1	openff-1.2.1	openff-1.3.0	gaff-2.11
Basis	smirnoff	smirnoff	smirnoff	smirnoff	smirnoff	antechamber
Wavefunction Protocol	none	none	none	none	none	none
Implicit Solvent
Keywords	{}	{}	{}	{}	{}	{}
Validated	✔️	✔️	✔️	✔️	✔️	✔️
Full Basis Coverage	✔️	✔️	✔️	✔️	✔️	✔️

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.21.0
rdkit	2021.03.4

jthorton

Great job @dotsdl, LGTM.

openff-dangerbot · 2021-08-13T17:46:41Z

QCSubmit Validation Report

	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2
Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
Elements	N ,F ,Cl ,O ,Br ,S ,H ,C ,P
Valid Cmiles	✔️
Connected Dihedrals	✔️
No Linear Torsions	✔️
No Molecular Complexes	✔️
Valid Constraints	✔️
Complete Metatdata	✔️
Valid SCF Properties	✔️

QC Specification Report

	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/smirnoff99Frosst-1.1.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.0.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.1.1	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.2.1	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-1.3.0	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/openff-2.0.0-rc.2	submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1/dataset.json.bz2/gaff-2.11
Specification Name	smirnoff99Frosst-1.1.0	openff-1.0.0	openff-1.1.1	openff-1.2.1	openff-1.3.0	openff-2.0.0-rc.2	gaff-2.11
Method	smirnoff99frosst-1.1.0	openff-1.0.0	openff-1.1.1	openff-1.2.1	openff-1.3.0	openff-2.0.0-rc.2	gaff-2.11
Basis	smirnoff	smirnoff	smirnoff	smirnoff	smirnoff	smirnoff	antechamber
Wavefunction Protocol	none	none	none	none	none	none	none
Implicit Solvent
Keywords	{}	{}	{}	{}	{}	{}	{}
Validated	✔️	✔️	✔️	✔️	✔️	✔️	✔️
Full Basis Coverage	✔️	✔️	✔️	✔️	✔️	✔️	✔️

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.21.0
rdkit	2021.03.4

openff-dangerbot · 2021-08-14T15:01:06Z

Lifecycle - QCSubmit Submission Report : SUCCESS


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-08-14 15:00 UTC

Response from public QCArchive:

{'smirnoff99Frosst-1.1.0': 0, 'openff-1.0.0': 0, 'openff-1.1.1': 0, 'openff-1.2.1': 0, 'openff-1.3.0': 0, 'openff-2.0.0-rc.2': 19655, 'gaff-2.11': 71655}

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.21.0
rdkit	2021.03.4

openff-dangerbot · 2021-08-15T19:24:00Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-08-15 19:17 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
smirnoff99Frosst-1.1.0	67043	4363	249
openff-1.0.0	56161	15323	171
openff-1.1.1	71336	82	237
openff-1.2.1	6888	64745	22
openff-1.3.0	4	71651	0
openff-2.0.0-rc.2	3	71652	0
gaff-2.11	1	71654	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 36

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1344, in create_openmm_system
parameter_handler.create_force(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 2929, in create_force
exception_cls=UnassignedBondParameterException,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 2487, in _check_all_valence_terms_assigned
raise exception
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedBondParameterException: BondHandler was not able to find parameters for the following valence terms:

- Topology indices (17, 18): names and elements (O4 O), (F1 F),




ids :
{'52098246', '52098262', '52098264', '52098265', '52098269', '52098270',
'52098365', '52098374', '52098384', '52098400', '52175698', '52175700',
'52175701', '52175705', '52175706', '52175810', '52175836', '52254518',
'52254534', '52254536', '52254537', '52254541', '52254542', '52254637',
'52254646', '52254656', '52254672', '52548906', '52548922', '52548924',
'52548929', '52548930', '52549125', '52549165', '52549175', '52549239'}
-------------------------------------
-------------------------------------
count : 28

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 8)




ids :
{'52111519', '52111520', '52111522', '52135655', '52135661', '52135667',
'52135669', '52135671', '52135683', '52148102', '52189682', '52189683',
'52189685', '52215028', '52215034', '52215040', '52215056', '52227305',
'52318018', '52318019', '52318021', '52411778', '52411784', '52411790',
'52411792', '52411794', '52411842', '52457790'}
-------------------------------------
-------------------------------------
count : 28

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 22)




ids :
{'52102514', '52102515', '52102516', '52102517', '52102518', '52102519',
'52102522', '52180090', '52180091', '52180092', '52180093', '52180094',
'52180095', '52180098', '52258896', '52258897', '52258898', '52258899',
'52258900', '52258901', '52258904', '52565371', '52565372', '52565373',
'52565374', '52565375', '52565415', '52565418'}
-------------------------------------
-------------------------------------
count : 27

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 2)
- Atom N (index 13)




ids :
{'52124840', '52124841', '52154635', '52154637', '52154640', '52154642',
'52154643', '52154644', '52154647', '52233849', '52233850', '52233851',
'52233854', '52233856', '52233857', '52233858', '52233861', '52370488',
'52370544', '52481854', '52481855', '52481856', '52481859', '52481861',
'52481862', '52481863', '52481866'}
-------------------------------------
-------------------------------------
count : 26

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 11)
- Atom N (index 32)




ids :
{'52130622', '52130624', '52150263', '52150264', '52150265', '52150269',
'52150270', '52150275', '52150280', '52150281', '52209498', '52209500',
'52229582', '52229583', '52229588', '52229593', '52393151', '52393214',
'52466095', '52466096', '52466097', '52466101', '52466102', '52466107',
'52466112', '52466113'}
-------------------------------------
-------------------------------------
count : 25

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1348, in create_openmm_system
parameter_handler.postprocess_system(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 3944, in postprocess_system
raise UnassignedMoleculeChargeException(msg)
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedMoleculeChargeException: The following molecules did not have charges assigned by any ParameterHandler in the ForceField:
[H][C]1=[C]2[C]([H])=[C]([H])[C]([c]3[c]([F])[c]([H])[c]([H])[c]([H])[c]3[F])=[N][N]2[C]([N]([H])[c]2[c]([H])[nH+][c]([H])[c]([H])[c]2[N]2[C]([H])([H])[C]([H])([H])[C]([H])([H])[C@]([H])([NH+]([H])[H])[C]2([H])[H])=[N]1




ids :
{'52128277', '52128281', '52128283', '52128285', '52129074', '52129076',
'52129078', '52129272', '52129276', '52207213', '52207215', '52208043',
'52208045', '52208178', '52222937', '52384180', '52384211', '52384213',
'52384215', '52387518', '52387520', '52387522', '52388603', '52388607',
'52440492'}
-------------------------------------
-------------------------------------
count : 25

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 9)
- Atom N (index 16)




ids :
{'52146994', '52146996', '52146997', '52147000', '52147002', '52147003',
'52147004', '52147007', '52147009', '52147011', '52226321', '52226323',
'52226324', '52226327', '52226336', '52226338', '52454089', '52454126',
'52454129', '52454131', '52454132', '52454133', '52454136', '52454138',
'52454140'}
-------------------------------------
-------------------------------------
count : 25

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 21)




ids :
{'52129672', '52129674', '52129676', '52129678', '52129684', '52129686',
'52129688', '52129692', '52129706', '52129720', '52208574', '52208576',
'52208578', '52208588', '52208590', '52390017', '52390019', '52390021',
'52390023', '52390061', '52390130', '52390132', '52390136', '52390197',
'52390211'}
-------------------------------------
-------------------------------------
count : 24

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1348, in create_openmm_system
parameter_handler.postprocess_system(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 3944, in postprocess_system
raise UnassignedMoleculeChargeException(msg)
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedMoleculeChargeException: The following molecules did not have charges assigned by any ParameterHandler in the ForceField:
[H][C]1=[N][N]([C]([H])([H])[H])[C]([H])=[C]1[c]1[n][c]([O][c]2[c]([H])[c]([N]([H])[C](=[O])[N]([H])[C]3=[C]([H])[C]([C]([H])([C]([H])([H])[H])[C]([H])([H])[H])=[N][N]3[c]3[c]([H])[c]([H])[c]([C]#[N])[c]([H])[c]3[H])[c]([F])[c]([H])[c]2[C]([H])([H])[H])[n][c]([H])[c]1[H]




ids :
{'52136815', '52136817', '52136823', '52136825', '52136827', '52136889',
'52136895', '52136968', '52216197', '52216199', '52216203', '52216205',
'52216207', '52216209', '52216277', '52415776', '52415778', '52415780',
'52415827', '52415829', '52415831', '52415845', '52415928', '52416182'}
-------------------------------------
-------------------------------------
count : 24

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 33)




ids :
{'52154133', '52154137', '52154138', '52154139', '52154140', '52154141',
'52154142', '52154151', '52154153', '52233423', '52233430', '52233431',
'52233432', '52233441', '52233443', '52480224', '52480228', '52480229',
'52480230', '52480231', '52480272', '52480273', '52480282', '52480284'}
-------------------------------------
-------------------------------------
count : 24

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 32)




ids :
{'52115443', '52115477', '52115479', '52115481', '52115483', '52115513',
'52115514', '52115515', '52193779', '52193813', '52193815', '52193817',
'52193819', '52193849', '52193850', '52193851', '52334842', '52334999',
'52335001', '52335144', '52335146', '52335176', '52335177', '52335178'}
-------------------------------------
-------------------------------------
count : 23

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1344, in create_openmm_system
parameter_handler.create_force(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 3183, in create_force
exception_cls=UnassignedProperTorsionParameterException,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 2487, in _check_all_valence_terms_assigned
raise exception
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedProperTorsionParameterException: ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (7, 17, 18, 10): names and elements (C8 C), (N4 N), (N5 N), (C11 C),




ids :
{'52117099', '52117100', '52117101', '52117102', '52117103', '52117104',
'52164001', '52164002', '52195580', '52195581', '52195582', '52195583',
'52195584', '52242880', '52242881', '52341391', '52341392', '52341428',
'52341429', '52341430', '52341431', '52509419', '52509420'}
-------------------------------------
-------------------------------------
count : 22

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 14)




ids :
{'52140151', '52140155', '52140167', '52140284', '52140288', '52140292',
'52140294', '52140296', '52140298', '52219687', '52219691', '52219693',
'52219697', '52426865', '52426869', '52426928', '52427590', '52427594',
'52427598', '52427600', '52427602', '52427604'}
-------------------------------------
-------------------------------------
count : 21

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/
--- Too many errors; truncated here ---

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.21.0
rdkit	2021.03.4

openff-dangerbot · 2021-08-16T13:16:06Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-08-16 13:05 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
smirnoff99Frosst-1.1.0	70834	587	234
openff-1.0.0	69453	1981	221
openff-1.1.1	71437	0	218
openff-1.2.1	71141	280	234
openff-1.3.0	36767	34762	126
openff-2.0.0-rc.2	9	71646	0
gaff-2.11	8	71647	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 50

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 21)




ids :
{'52129672', '52129674', '52129676', '52129678', '52129684', '52129686',
'52129688', '52129692', '52129706', '52129720', '52208574', '52208576',
'52208578', '52208580', '52208586', '52208588', '52208590', '52208594',
'52208608', '52208622', '52390017', '52390019', '52390021', '52390023',
'52390061', '52390130', '52390132', '52390136', '52390197', '52390211',
'52670263', '52670265', '52670267', '52670269', '52670275', '52670277',
'52670279', '52670283', '52670327', '52670341', '52951719', '52951721',
'52951723', '52951824', '52951918', '52951920', '52951922', '52951967',
'52951981', '52951995'}
-------------------------------------
-------------------------------------
count : 49

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 8)




ids :
{'52111519', '52111520', '52111522', '52135655', '52135661', '52135667',
'52135669', '52135671', '52135683', '52148102', '52189682', '52189683',
'52189685', '52215028', '52215034', '52215040', '52215042', '52215044',
'52215056', '52227305', '52318018', '52318019', '52318021', '52411778',
'52411784', '52411790', '52411792', '52411794', '52411842', '52457790',
'52599067', '52599068', '52599070', '52693791', '52693826', '52693832',
'52693860', '52693862', '52693874', '52737414', '52879736', '52879737',
'52879739', '52975153', '52975236', '52975242', '52975244', '52975287',
'52975299'}
-------------------------------------
-------------------------------------
count : 48

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1348, in create_openmm_system
parameter_handler.postprocess_system(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 3944, in postprocess_system
raise UnassignedMoleculeChargeException(msg)
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedMoleculeChargeException: The following molecules did not have charges assigned by any ParameterHandler in the ForceField:
[H][C]1=[C]2[C]([H])=[C]([H])[C]([c]3[c]([F])[c]([H])[c]([H])[c]([H])[c]3[F])=[N][N]2[C]([N]([H])[c]2[c]([H])[nH+][c]([H])[c]([H])[c]2[N]2[C]([H])([H])[C]([H])([H])[C]([H])([H])[C@]([H])([NH+]([H])[H])[C]2([H])[H])=[N]1




ids :
{'52128277', '52128281', '52128283', '52128285', '52129074', '52129076',
'52129078', '52129272', '52129276', '52143492', '52207207', '52207211',
'52207213', '52207215', '52208043', '52208045', '52208047', '52208174',
'52208178', '52222937', '52384180', '52384211', '52384213', '52384215',
'52387518', '52387520', '52387522', '52388603', '52388607', '52440492',
'52664532', '52664538', '52664540', '52667132', '52667134', '52667136',
'52668445', '52668490', '52721913', '52946204', '52946239', '52946241',
'52946243', '52949055', '52949057', '52949059', '52950043', '52950047'}
-------------------------------------
-------------------------------------
count : 47

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1344, in create_openmm_system
parameter_handler.create_force(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 2929, in create_force
exception_cls=UnassignedBondParameterException,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 2487, in _check_all_valence_terms_assigned
raise exception
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedBondParameterException: BondHandler was not able to find parameters for the following valence terms:

- Topology indices (17, 18): names and elements (O4 O), (F1 F),




ids :
{'52098246', '52098262', '52098264', '52098265', '52098269', '52098270',
'52098365', '52098374', '52098384', '52098400', '52175682', '52175700',
'52175701', '52175705', '52175706', '52175801', '52175810', '52175836',
'52254518', '52254534', '52254536', '52254537', '52254541', '52254542',
'52254637', '52254646', '52254656', '52254672', '52548906', '52548922',
'52548924', '52548925', '52548929', '52548930', '52549165', '52549175',
'52549239', '52831720', '52831773', '52831775', '52831776', '52831780',
'52831781', '52832210', '52832240', '52832250', '52832266'}
-------------------------------------
-------------------------------------
count : 42

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 2)
- Atom N (index 13)




ids :
{'52124840', '52124841', '52154635', '52154636', '52154637', '52154640',
'52154642', '52154643', '52154644', '52154647', '52203513', '52203514',
'52233849', '52233850', '52233851', '52233854', '52233856', '52233857',
'52233858', '52233861', '52370488', '52370544', '52481854', '52481855',
'52481856', '52481859', '52481861', '52481862', '52481863', '52481866',
'52650372', '52650373', '52760785', '52760786', '52760787', '52760790',
'52760792', '52760793', '52760794', '52760797', '52931684', '52931720'}
-------------------------------------
-------------------------------------
count : 40

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 32)




ids :
{'52115443', '52115477', '52115479', '52115481', '52115483', '52115513',
'52115514', '52115515', '52193779', '52193813', '52193815', '52193817',
'52193819', '52193849', '52193850', '52193851', '52334842', '52334999',
'52335001', '52335144', '52335146', '52335176', '52335177', '52335178',
'52614569', '52614718', '52614765', '52614767', '52614769', '52614887',
'52614888', '52614889', '52895872', '52895906', '52895954', '52895956',
'52895958', '52896162', '52896189', '52896254'}
-------------------------------------
-------------------------------------
count : 40

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 11)
- Atom N (index 32)




ids :
{'52130622', '52130624', '52150263', '52150264', '52150265', '52150269',
'52150270', '52150275', '52150280', '52150281', '52209498', '52209500',
'52229576', '52229577', '52229578', '52229582', '52229583', '52229588',
'52229593', '52229594', '52393151', '52393214', '52466095', '52466096',
'52466097', '52466101', '52466102', '52466107', '52466112', '52466113',
'52673144', '52673218', '52745813', '52745815', '52745819', '52745825',
'52745830', '52745831', '52955406', '52955408'}
-------------------------------------
-------------------------------------
count : 39

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 9)
- Atom N (index 16)




ids :
{'52146994', '52146996', '52146997', '52147000', '52147002', '52147003',
'52147004', '52147007', '52147009', '52147011', '52226321', '52226323',
'52226324', '52226327', '52226329', '52226330', '52226331', '52226336',
'52226338', '52454087', '52454089', '52454126', '52454129', '52454131',
'52454132', '52454133', '52454136', '52454138', '52454140', '52733974',
'52733976', '52733977', '52733980', '52733982', '52733983', '52733984',
'52733987', '52733989', '52733991'}
-------------------------------------
-------------------------------------
count : 39

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 5)
- Atom N (index 22)




ids :
{'52133372', '52133374', '52133378', '52133380', '52133382', '52133386',
'52133402', '52133406', '52212388', '52212390', '52212394', '52212396',
'52212398', '52212402', '52212418', '52212422', '52403234', '52403236',
'52403240', '52403242', '52403244', '52403294', '52403310', '52403314',
'52684912', '52684914', '52684918', '52684920', '52684922', '52684966',
'52685003', '52685007', '52965802', '52965808', '52965810', '52965812',
'52965816', '52965899', '52965903'}
-------------------------------------
-------------------------------------
count : 38

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1348, in create_openmm_system
parameter_handler.postprocess_system(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 3944, in postprocess_system
raise UnassignedMoleculeChargeException(msg)
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedMoleculeChargeException: The following molecules did not have charges assigned by any ParameterHandler in the ForceField:
[H]/[NH+]=[C](\[c]1[c]([H])[c]([H])[c]2[c]([H])[c]([C](=[O])[N]([H])[c]3[c]([H])[c]([H])[c]([C]([H])([H])[NH+]([H])[H])[c]([H])[c]3[H])[c]([H])[c]([H])[c]2[c]1[H])[N]([H])[H]




ids :
{'52127952', '52128833', '52128835', '52128837', '52128976', '52128978',
'52143579', '52145581', '52206799', '52207802', '52207804', '52207806',
'52207945', '52207947', '52223024', '52224942', '52382781', '52386136',
'52386138', '52386140', '52386771', '52386773', '52440925', '52448587',
'52663280', '52666318', '52666320', '52666322', '52666882', '52666884',
'52722314', '52729605', '52944633', '52948149', '52948151', '52948153',
'52948737', '52948739'}
-------------------------------------
-------------------------------------
count : 38

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 6)
- Atom N (index 13)




ids :
{'52123554', '52123556', '52123557', '52123559', '52123560', '52123561',
'52123565', '52123567', '52202196', '52202198', '52202201', '52202202',
'52202207', '52202209', '52365544', '52365546', '52365547', '52365549',
'52365550', '52365551', '52365555', '52365557', '52645452', '52645454',
'52645455', '52645457', '52645458', '52645459', '52645522', '52645524',
'52927786', '52927788', '52927789', '52927791', '52927792', '52927793',
'52927797', '52927799'}
-------------------------------------
-------------------------------------
count : 36

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1344, in create_openmm_system
parameter_handler.create_force(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 3183, in create_force
exception_cls=UnassignedProperTorsionParameterException,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 2487, in _check_all_valence_terms_assigned
raise exception
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedProperTorsionParameterException: ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (7, 17, 18, 10): names and elements (C8 C), (N4 N), (N5 N), (C11 C),




ids :
{'52117099', '52117100', '52117101', '52117102', '52117103', '52117104',
'52164001', '52164002', '52195580', '52195581', '52195582', '52195583',
'52195584', '52195585', '52242880', '52242881', '52341391', '52341392',
'52341428', '52341430', '52341431', '52509419', '52509420', '52622110',
'52622111', '52622112', '52622113', '52622114', '52622115', '52793113',
'52793114', '52903659', '52903660', '52903698', '52903718', '52903719'}
-------------------------------------
-------------------------------------
count : 36

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 33)




ids :
{'52154133', '52154137', '52154138', '52154139', '52154140', '52154141',
'52154142', '52154151', '52154153', '52233423', '52233427', '52233428',
'52233429', '52233430', '52233431', '52233432', '52233441', '52233443',
'52480224', '52480228', '52480229', '52480230', '52480231', '52480272',
'52480273', '52480282', '52480284', '52759139', '52759172', '52759173',
'52759174', '52759175', '52759176', '52759177', '52759186', '52759214'}
-------------------------------------
-------------------------------------
count : 35

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive
--- Too many errors; truncated here ---

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.21.0
rdkit	2021.03.4

openff-dangerbot · 2021-08-17T23:52:04Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-08-17 23:51 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
smirnoff99Frosst-1.1.0	71348	83	224
openff-1.0.0	71243	190	222
openff-1.1.1	71440	0	215
openff-1.2.1	71373	67	215
openff-1.3.0	71423	3	229
openff-2.0.0-rc.2	71417	5	233
gaff-2.11	71428	16	211

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 70

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 2)
- Atom N (index 13)




ids :
{'52124840', '52124841', '52154635', '52154636', '52154637', '52154640',
'52154642', '52154643', '52154644', '52154647', '52203513', '52203514',
'52233849', '52233850', '52233851', '52233854', '52233856', '52233857',
'52233858', '52233861', '52370488', '52370544', '52481854', '52481855',
'52481856', '52481859', '52481861', '52481862', '52481863', '52481866',
'52650372', '52650373', '52760785', '52760786', '52760787', '52760790',
'52760792', '52760793', '52760794', '52760797', '52931684', '52931720',
'53035032', '53035059', '53035060', '53035063', '53035065', '53035066',
'53035072', '53035135', '53224775', '53224776', '54929313', '54929314',
'54929315', '54929355', '54929357', '54929412', '54929413', '54929416',
'55250957', '55250958', '55280859', '55280860', '55280861', '55280864',
'55280866', '55280867', '55280868', '55280871'}
-------------------------------------
-------------------------------------
count : 69

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 9)
- Atom N (index 16)




ids :
{'52146994', '52146996', '52146997', '52147000', '52147002', '52147003',
'52147004', '52147007', '52147009', '52147011', '52226321', '52226323',
'52226324', '52226327', '52226329', '52226330', '52226331', '52226334',
'52226336', '52226338', '52454087', '52454089', '52454126', '52454129',
'52454131', '52454132', '52454133', '52454136', '52454138', '52454140',
'52733974', '52733976', '52733977', '52733980', '52733982', '52733983',
'52733984', '52733987', '52733989', '52733991', '53013152', '53013154',
'53013155', '53013158', '53013160', '53013161', '53013162', '53013165',
'53013167', '53013169', '53317884', '53317886', '53317887', '53317890',
'53317892', '53317893', '53317894', '53317897', '53317899', '53317901',
'55273726', '55273728', '55273729', '55273732', '55273734', '55273735',
'55273739', '55273741', '55273743'}
-------------------------------------
-------------------------------------
count : 69

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 11)
- Atom N (index 32)




ids :
{'52130622', '52130624', '52150263', '52150264', '52150265', '52150269',
'52150270', '52150275', '52150280', '52150281', '52209498', '52209500',
'52229576', '52229577', '52229578', '52229582', '52229583', '52229588',
'52229593', '52229594', '52393151', '52393214', '52466095', '52466096',
'52466101', '52466102', '52466107', '52466112', '52466113', '52673144',
'52673218', '52745813', '52745814', '52745815', '52745819', '52745820',
'52745825', '52745830', '52745831', '52955406', '52955408', '53022994',
'53022995', '53022996', '53023000', '53023001', '53023006', '53023049',
'53023050', '53244189', '53244191', '53330043', '53330044', '53330045',
'53330049', '53330050', '53330107', '53330159', '53330179', '55257252',
'55257254', '55276783', '55276784', '55276785', '55276789', '55276790',
'55276795', '55276800', '55276801'}
-------------------------------------
-------------------------------------
count : 68

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 8)




ids :
{'52111519', '52111520', '52111522', '52135655', '52135661', '52135667',
'52135669', '52135671', '52135683', '52148102', '52189682', '52189683',
'52189685', '52215028', '52215034', '52215040', '52215042', '52215044',
'52215056', '52227305', '52318018', '52318019', '52318021', '52411778',
'52411784', '52411790', '52411792', '52411794', '52411842', '52457790',
'52599067', '52599068', '52599070', '52693791', '52693826', '52693832',
'52693860', '52693862', '52693874', '52737414', '52879736', '52879737',
'52879739', '52975153', '52975236', '52975242', '52975244', '52975287',
'52975299', '53016732', '53170714', '53170715', '53170717', '53272297',
'53272357', '53272359', '53272361', '53272420', '55201392', '55201393',
'55201395', '55262725', '55262731', '55262737', '55262739', '55262741',
'55262753', '55274776'}
-------------------------------------
-------------------------------------
count : 68

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 21)




ids :
{'52129674', '52129676', '52129678', '52129684', '52129686', '52129688',
'52129692', '52129706', '52129720', '52208574', '52208576', '52208578',
'52208580', '52208586', '52208588', '52208590', '52208594', '52208608',
'52208622', '52390017', '52390019', '52390021', '52390023', '52390061',
'52390130', '52390132', '52390136', '52390197', '52390211', '52670263',
'52670265', '52670267', '52670269', '52670277', '52670279', '52670283',
'52670327', '52670341', '52951719', '52951721', '52951723', '52951824',
'52951918', '52951920', '52951922', '52951967', '52951981', '52951995',
'53240448', '53240450', '53240452', '53240454', '53240512', '53240514',
'53240516', '53240559', '53240620', '53240732', '55256249', '55256251',
'55256253', '55256255', '55256261', '55256263', '55256265', '55256269',
'55256283', '55256297'}
-------------------------------------
-------------------------------------
count : 63

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 14)




ids :
{'52140151', '52140155', '52140167', '52140284', '52140288', '52140292',
'52140294', '52140296', '52140298', '52219550', '52219554', '52219566',
'52219683', '52219687', '52219691', '52219693', '52219695', '52219697',
'52426865', '52426869', '52426928', '52427590', '52427594', '52427598',
'52427600', '52427602', '52427604', '52710003', '52710007', '52710019',
'52710360', '52710364', '52710368', '52710370', '52710372', '52710374',
'52990437', '52990441', '52990453', '52991073', '52991077', '52991142',
'52991144', '52991146', '52991148', '53291399', '53291452', '53291464',
'53291995', '53291999', '53292003', '53292005', '53292007', '53292009',
'55267185', '55267189', '55267201', '55267318', '55267322', '55267362',
'55267364', '55267366', '55267368'}
-------------------------------------
-------------------------------------
count : 61

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 33)




ids :
{'52154133', '52154137', '52154138', '52154139', '52154140', '52154141',
'52154142', '52154151', '52154153', '52233423', '52233427', '52233428',
'52233429', '52233430', '52233431', '52233432', '52233441', '52233443',
'52480224', '52480228', '52480229', '52480230', '52480231', '52480272',
'52480273', '52480282', '52480284', '52759139', '52759172', '52759173',
'52759174', '52759175', '52759176', '52759186', '52759214', '53033363',
'53033367', '53033368', '53033369', '53033370', '53033371', '53033372',
'53033381', '53033383', '54926256', '54926295', '54926343', '54926344',
'54926346', '54926347', '54926356', '54926358', '55280433', '55280437',
'55280438', '55280439', '55280440', '55280441', '55280442', '55280451',
'55280453'}
-------------------------------------
-------------------------------------
count : 59

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1344, in create_openmm_system
parameter_handler.create_force(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 2929, in create_force
exception_cls=UnassignedBondParameterException,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 2487, in _check_all_valence_terms_assigned
raise exception
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedBondParameterException: BondHandler was not able to find parameters for the following valence terms:

- Topology indices (17, 18): names and elements (O4 O), (F1 F),




ids :
{'52098246', '52098262', '52098264', '52098265', '52098269', '52098270',
'52098365', '52098374', '52098384', '52098400', '52175682', '52175698',
'52175700', '52175701', '52175705', '52175706', '52175801', '52175810',
'52175820', '52175836', '52254518', '52254534', '52254536', '52254537',
'52254541', '52254542', '52254637', '52254646', '52254656', '52254672',
'52548906', '52548922', '52548924', '52548925', '52548929', '52548930',
'52549125', '52549165', '52549175', '52549239', '52831720', '52831773',
'52831775', '52831776', '52831780', '52831781', '52832210', '52832240',
'52832250', '52832266', '53124378', '53124507', '53124509', '53124510',
'53124554', '53124866', '53124914', '53124963', '53125079'}
-------------------------------------
-------------------------------------
count : 58

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 236, in compute
molecule=off_mol, method=input_model.model.method, keywords=input_model.keywords
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 183, in _generate_openmm_system
system = system_generator.create_system(topology=topology.to_openmm(), molecules=[molecule])
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/system_generators.py", line 324, in create_system
system = self.forcefield.createSystem(topology, **forcefield_kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1179, in createSystem
templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1383, in _matchAllResiduesToTemplates
if generator(self, res):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 304, in generator
ffxml_contents = self.generate_residue_template(molecule)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 1154, in generate_residue_template
system = self._smirnoff_forcefield.create_openmm_system(molecule.to_topology(), charge_from_molecules=charge_from_molecules)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1348, in create_openmm_system
parameter_handler.postprocess_system(system, topology, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/typing/engines/smirnoff/parameters.py", line 3944, in postprocess_system
raise UnassignedMoleculeChargeException(msg)
openff.toolkit.typing.engines.smirnoff.parameters.UnassignedMoleculeChargeException: The following molecules did not have charges assigned by any ParameterHandler in the ForceField:
[H][C]1=[C]2[C]([H])=[C]([H])[C]([c]3[c]([F])[c]([H])[c]([H])[c]([H])[c]3[F])=[N][N]2[C]([N]([H])[c]2[c]([H])[nH+][c]([H])[c]([H])[c]2[N]2[C]([H])([H])[C]([H])([H])[C]([H])([H])[C@]([H])([NH+]([H])[H])[C]2([H])[H])=[N]1




ids :
{'52128277', '52128281', '52128285', '52129074', '52129076', '52129078',
'52129272', '52129276', '52143492', '52207207', '52207211', '52207213',
'52207215', '52208043', '52208045', '52208047', '52208174', '52208178',
'52222937', '52384180', '52384211', '52384213', '52384215', '52387518',
'52387520', '52387522', '52388603', '52388607', '52440492', '52664532',
'52664536', '52664538', '52664540', '52667132', '52667134', '52667136',
'52668445', '52668490', '52721913', '52946204', '52946239', '52946241',
'52946243', '52949055', '52949057', '52949059', '52950043', '52950047',
'53001977', '53235573', '53235635', '53235676', '53235678', '53238030',
'53238032', '53238034', '53238918', '53304670'}
-------------------------------------
-------------------------------------
count : 56

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 32)




ids :
{'52115443', '52115477', '52115479', '52115481', '52115483', '52115513',
'52115514', '52115515', '52193779', '52193813', '52193815', '52193817',
'52193819', '52193849', '52193850', '52193851', '52334842', '52334999',
'52335001', '52335144', '52335146', '52335176', '52335177', '52335178',
'52614569', '52614718', '52614765', '52614767', '52614769', '52614887',
'52614888', '52614889', '52895872', '52895906', '52895954', '52895956',
'52895958', '52896162', '52896189', '52896254', '53181679', '53181713',
'53181715', '53181717', '53181719', '53181823', '53181824', '53181825',
'55228339', '55228659', '55228661', '55228663', '55228665', '55228852',
'55228853', '55228854'}
-------------------------------------
-------------------------------------
count : 55

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 6)
- Atom N (index 13)




ids :
{'52123554', '52123556', '52123557', '52123559', '52123560', '52123561',
'52123565', '52123567', '52202196', '52202198', '52202199', '52202201',
'52202202', '52202203', '52202207', '52202209', '52365544', '52365547',
'52365549', '52365550', '52365551', '52365555', '52365557', '52645452',
'52645454', '52645455', '52645457', '52645458', '52645459', '52645522',
'52645524', '52927786', '52927788', '52927789', '52927791', '52927792',
'52927793', '52927797', '52927799', '53219479', '53219481', '53219482',
'53219484', '53219485', '53219486', '53219490', '53219492', '55249289',
'55249291', '55249292', '55249294', '55249295', '55249296', '55249300',
'55249302'}
-------------------------------------
-------------------------------------
count : 54

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 53)




ids :
{'52148287', '52148288', '52148290', '52148292', '52148294', '52148295',
'52148297', '52148308', '52227538', '52227539', '52227541', '52227543',
'52227545', '52227546', '52227548', '52227559', '52458749', '52458750',
'52458752', '52458846', '52458848', '52458849', '52458851', '52738243',
'52738244', '52738246', '52738392', '52738394', '52738517', '52738519',
'52738558', '53017455', '53017456', '53017458', '53017460', '53017462',
'53017463', '53017465', '53017476', '53322688', '53322689', '53322691',
'53322693', '53322696', '53322734', '53322895', '55274961', '55274962',
'55274964', '55274966', '55274968', '55274969', '55274971', '55274982'}
-------------------------------------
-------------------------------------
count : 54

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1293, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Execution Error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/qcengine/programs/openmm.py", line 223, in compute
off_mol = offtop.Molecule.from_mapped_smiles(mapped_smiles=cmiles)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5303, in from_mapped_smiles
allow_undefined_stereo=allow_undefined_stereo,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 2928, in from_smiles
_cls=cls,
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 367, in call
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 363, in call
return method(*args, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 774, in from_smiles
rdmol, err_msg_prefix="Unable to make OFFMol from SMILES: "
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-openmm-2021-08-12/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2218, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from SMILES: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom N (index 5)
- Atom N (index 22)




ids :
{'52133372', '52133374', '52133378', '52133380', '52133382', '52133386',
'52133402', '52133406', '52212388', '52212390', '52212394', '52212396',
'52212398', '52212402', '52212418', '52212422', '52403234', '52403236',
'524032
--- Too many errors; truncated here ---

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.21.0
rdkit	2021.03.4

openff-dangerbot · 2021-09-14T02:54:44Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-14 02:54 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	ERROR
smirnoff99Frosst-1.1.0	71436	219
openff-1.0.0	71439	216
openff-1.1.1	71443	212
openff-1.2.1	71443	212
openff-1.3.0	71435	220
openff-2.0.0-rc.2	71437	218
gaff-2.11	71463	192

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1486

None

ids :
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'55298316', '55298317', '55298319', '55298320'}
-------------------------------------
-------------------------------------
count : 2

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53304995', '53312831'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53312391'}
-------------------------------------

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.22.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-14T13:00:45Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-14 13:00 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	ERROR
smirnoff99Frosst-1.1.0	71441	214
openff-1.0.0	71445	210
openff-1.1.1	71444	211
openff-1.2.1	71444	211
openff-1.3.0	71446	209
openff-2.0.0-rc.2	71447	208
gaff-2.11	71469	186

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1446

None

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'53189004', '53189005', '53189006', '53189007', '53189008', '53189009',
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'53240454', '53240512', '53240514', '53240516', '53240559', '53240620',
'53240732', '53244189', '53244191', '53247047', '53247119', '53247121',
'53247801', '53247803', '53247805', '53247817', '53251601', '53258345',
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'53270950', '53270954', '53270994', '53272297', '53272351', '53272357',
'53272359', '53272361', '53272420', '53283481', '53283485', '53283487',
'53283559', '53287506', '53291399', '53291452', '53291464', '53291995',
'53291999', '53292003', '53292005', '53292007', '53292009', '53296508',
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'53317890', '53317892', '53317893', '53317894', '53317897', '53317899',
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'55120066', '55120101', '55120102', '55120130', '55120131', '55120132',
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'55290779', '55290780', '55290782', '55293668', '55293675', '55293676',
'55298313', '55298315', '55298316', '55298317', '55298319', '55298320'}
-------------------------------------
-------------------------------------
count : 2

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53312831', '53304995'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53312391'}
-------------------------------------

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.22.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-15T12:56:53Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-15 12:56 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
smirnoff99Frosst-1.1.0	71442	2	211
openff-1.0.0	71446	0	209
openff-1.1.1	71446	0	209
openff-1.2.1	71448	0	207
openff-1.3.0	71447	0	208
openff-2.0.0-rc.2	71448	0	207
gaff-2.11	71476	0	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1427

None

ids :
{'52098246', '52098262', '52098264', '52098265', '52098269', '52098270',
'52098365', '52098374', '52098384', '52098400', '52099606', '52099675',
'52099683', '52102514', '52102515', '52102516', '52102517', '52102518',
'52102519', '52102522', '52107213', '52111519', '52111520', '52111522',
'52115443', '52115477', '52115479', '52115481', '52115483', '52115513',
'52115514', '52115515', '52117099', '52117100', '52117101', '52117102',
'52117103', '52117104', '52117806', '52117807', '52117813', '52123554',
'52123556', '52123557', '52123559', '52123560', '52123561', '52123565',
'52123567', '52124840', '52124841', '52126609', '52126696', '52126735',
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'55298315', '55298316', '55298317', '55298319', '55298320'}
-------------------------------------
-------------------------------------
count : 2

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53304995', '53312831'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53312391'}
-------------------------------------

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.2
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.22.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-16T12:53:16Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-16 12:52 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.22.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-17T12:50:19Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-17 12:49 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.22.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-22T22:03:09Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-22 22:02 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.22.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-23T12:57:54Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-23 12:57 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.22.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-24T12:52:36Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-24 12:52 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-25T12:52:52Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-25 12:52 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-26T12:52:32Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-26 12:52 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-27T13:02:20Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-27 13:01 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-28T12:57:01Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-28 12:56 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE	ERROR
smirnoff99Frosst-1.1.0	71442	212	1
openff-1.0.0	71446	209	0
openff-1.1.1	71446	209	0
openff-1.2.1	71448	207	0
openff-1.3.0	71447	208	0
openff-2.0.0-rc.2	71448	207	0
gaff-2.11	71476	179	0

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1

None

ids :
{'52098246'}
-------------------------------------

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-29T12:55:17Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-29 12:54 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-09-30T13:27:32Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-09-30 13:27 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-10-01T13:10:28Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-10-01 13:09 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-10-02T12:58:59Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-10-02 12:58 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-10-03T13:09:55Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-10-03 13:09 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-10-04T13:57:03Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-10-04 13:56 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-10-06T13:10:48Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-10-06 13:10 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	INCOMPLETE
smirnoff99Frosst-1.1.0	71442	213
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71476	179

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-10-07T13:08:33Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-10-07 13:08 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	ERROR
smirnoff99Frosst-1.1.0	71443	212
openff-1.0.0	71446	209
openff-1.1.1	71446	209
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71477	178

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1427

None

ids :
{'52098246', '52098262', '52098264', '52098265', '52098269', '52098270',
'52098365', '52098374', '52098384', '52098400', '52099606', '52099675',
'52099683', '52102514', '52102515', '52102516', '52102517', '52102518',
'52102519', '52102522', '52107210', '52107213', '52111519', '52111520',
'52111522', '52115443', '52115477', '52115479', '52115481', '52115483',
'52115513', '52115514', '52115515', '52117099', '52117100', '52117101',
'52117102', '52117103', '52117104', '52117806', '52117807', '52117813',
'52123554', '52123556', '52123557', '52123559', '52123560', '52123561',
'52123565', '52123567', '52124840', '52124841', '52126609', '52126696',
'52126735', '52126737', '52126754', '52127952', '52128277', '52128281',
'52128283', '52128285', '52128833', '52128835', '52128837', '52128976',
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'55298315', '55298316', '55298317', '55298319', '55298320'}
-------------------------------------
-------------------------------------
count : 2

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53312831', '53304995'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53312391'}
-------------------------------------

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

openff-dangerbot · 2021-10-08T13:06:42Z

Lifecycle - Error Cycling Report


Dataset Name	OpenFF Industry Benchmark Season 1 - MM v1.1
Dataset Type	OptimizationDataset
UTC Datetime	2021-10-08 13:06 UTC

All errored tasks will be restarted.
Errored states prior to restart reported below.

`OptimizationRecord` current status

specification	COMPLETE	ERROR
smirnoff99Frosst-1.1.0	71444	211
openff-1.0.0	71446	209
openff-1.1.1	71447	208
openff-1.2.1	71448	207
openff-1.3.0	71447	208
openff-2.0.0-rc.2	71448	207
gaff-2.11	71477	178

`OptimizationRecord` Error Tracebacks:

Tracebacks (click to expand)

-------------------------------------
count : 1425

None

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'53033381', '53033383', '53035032', '53035059', '53035060', '53035063',
'53035065', '53035066', '53035072', '53035135', '53069267', '53069268',
'53069269', '53069270', '53069271', '53073760', '53073761', '53080836',
'53080837', '53080839', '53095563', '53095570', '53095571', '53117213',
'53117273', '53117305', '53117306', '53117308', '53117309', '53124378',
'53124507', '53124509', '53124510', '53124553', '53124554', '53124866',
'53124914', '53124963', '53125079', '53130263', '53130620', '53130628',
'53142293', '53142294', '53142295', '53142296', '53142297', '53142298',
'53142301', '53170714', '53170715', '53170717', '53181679', '53181713',
'53181715', '53181717', '53181719', '53181823', '53181824', '53181825',
'53189004', '53189005', '53189006', '53189007', '53189008', '53189009',
'53191948', '53191949', '53191955', '53219479', '53219481', '53219482',
'53219484', '53219485', '53219486', '53219490', '53219492', '53224775',
'53224776', '53229950', '53230071', '53230110', '53230112', '53230129',
'53234617', '53235573', '53235635', '53235676', '53235678', '53236952',
'53236954', '53236956', '53237408', '53237410', '53238030', '53238032',
'53238034', '53238914', '53238918', '53240448', '53240450', '53240452',
'53240454', '53240512', '53240514', '53240516', '53240559', '53240620',
'53240732', '53244189', '53244191', '53247047', '53247119', '53247121',
'53247801', '53247803', '53247805', '53247817', '53251601', '53258345',
'53258347', '53258406', '53258408', '53258488', '53258492', '53258508',
'53258512', '53259754', '53270938', '53270940', '53270942', '53270944',
'53270950', '53270954', '53270994', '53272297', '53272351', '53272357',
'53272359', '53272361', '53272420', '53283481', '53283485', '53283487',
'53283559', '53291399', '53291452', '53291464', '53291995', '53291999',
'53292003', '53292005', '53292007', '53292009', '53296508', '53296510',
'53304670', '53304776', '53304778', '53309679', '53310608', '53310662',
'53310682', '53312671', '53317884', '53317886', '53317887', '53317890',
'53317892', '53317893', '53317894', '53317897', '53317899', '53317901',
'53321997', '53322688', '53322689', '53322691', '53322693', '53322695',
'53322696', '53322734', '53322895', '53327482', '53327484', '53327494',
'53327513', '53327517', '53330043', '53330044', '53330045', '53330049',
'53330050', '53330107', '53330159', '53330179', '53332885', '54926256',
'54926295', '54926343', '54926344', '54926345', '54926346', '54926347',
'54926356', '54926358', '54929313', '54929314', '54929315', '54929355',
'54929357', '54929412', '54929413', '54929416', '54986069', '54986106',
'54986107', '54986108', '54986109', '54993870', '54993871', '55007179',
'55007180', '55007182', '55033238', '55033245', '55033246', '55070689',
'55070757', '55070758', '55070759', '55070761', '55070762', '55120066',
'55120101', '55120102', '55120130', '55120131', '55120132', '55120203',
'55201392', '55201393', '55201395', '55228339', '55228659', '55228661',
'55228663', '55228665', '55228852', '55228853', '55228854', '55239124',
'55239125', '55239131', '55249289', '55249291', '55249292', '55249294',
'55249295', '55249296', '55249300', '55249302', '55250957', '55250958',
'55252833', '55252959', '55252998', '55253000', '55253017', '55254360',
'55254786', '55254790', '55254792', '55254794', '55255332', '55255334',
'55255336', '55255536', '55255538', '55255634', '55255636', '55255638',
'55255786', '55255790', '55256249', '55256251', '55256253', '55256255',
'55256261', '55256263', '55256265', '55256269', '55256283', '55256297',
'55257252', '55257254', '55258098', '55258106', '55258108', '55258112',
'55258114', '55258116', '55258128', '55260242', '55260244', '55260248',
'55260250', '55260252', '55260256', '55260272', '55260276', '55262431',
'55262433', '55262435', '55262437', '55262443', '55262447', '55262449',
'55262725', '55262731', '55262737', '55262739', '55262741', '55262753',
'55265301', '55265305', '55265307', '55265333', '55267185', '55267189',
'55267201', '55267318', '55267322', '55267362', '55267364', '55267366',
'55267368', '55268845', '55268847', '55270435', '55270453', '55270455',
'55270522', '55271693', '55271904', '55271910', '55271930', '55272385',
'55272476', '55272508', '55273726', '55273728', '55273729', '55273732',
'55273734', '55273735', '55273736', '55273739', '55273741', '55273743',
'55274776', '55274961', '55274962', '55274964', '55274966', '55274968',
'55274969', '55274971', '55274982', '55276783', '55276784', '55276785',
'55276789', '55276790', '55276795', '55276800', '55276801', '55280433',
'55280437', '55280438', '55280439', '55280440', '55280441', '55280442',
'55280451', '55280453', '55280859', '55280860', '55280861', '55280864',
'55280866', '55280867', '55280868', '55280871', '55288052', '55288053',
'55288054', '55288055', '55288056', '55290779', '55290780', '55290782',
'55293668', '55293675', '55293676', '55298313', '55298315', '55298316',
'55298317', '55298319', '55298320'}
-------------------------------------
-------------------------------------
count : 2

geomeTRIC run_json error:
Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/home/dotson/.miniconda3/envs/qcarchive-worker-openff-psi4/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53312831', '53304995'}
-------------------------------------
-------------------------------------
count : 1

geomeTRIC run_json error:
Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/run_json.py", line 214, in geometric_run_json
geometric.optimize.Optimize(coords, M, IC, engine, None, params)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1331, in Optimize
return optimizer.optimizeGeometry()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1298, in optimizeGeometry
self.calcEnergyForce()
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/optimize.py", line 1002, in calcEnergyForce
spcalc = self.engine.calc(self.X, self.dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 873, in calc
return self.calc_new(coords, dirname)
File "/opt/conda/envs/qcfractal/lib/python3.7/site-packages/geometric/engine.py", line 865, in calc_new
raise QCEngineAPIEngineError("QCEngineAPI computation did not execute correctly. Message: " + ret["error"]["error_message"])
geometric.errors.QCEngineAPIEngineError: QCEngineAPI computation did not execute correctly. Message: QCEngine Unknown Error: Traceback (most recent call last):
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 411, in run_qcschema
ret_data = run_json_qcschema(input_model.dict(), clean, False, keep_wfn=keep_wfn)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/schema_wrapper.py", line 558, in run_json_qcschema
val, wfn = methods_dict_[json_data["driver"]](method, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/driver.py", line 717, in gradient
wfn = procedures['gradient'][lowername](lowername, molecule=molecule, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2383, in run_scf_gradient
ref_wfn = run_scf(name, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 2288, in run_scf
scf_wfn = scf_helper(name, post_scf=False, **kwargs)
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/proc.py", line 1568, in scf_helper
e_scf = scf_wfn.compute_energy()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 93, in scf_compute_energy
raise e
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 86, in scf_compute_energy
self.iterations()
File "/opt/conda/envs/qcfractal/lib//python3.7/site-packages/psi4/driver/procrouting/scf_proc/scf_iterator.py", line 464, in scf_iterate
raise SCFConvergenceError("""SCF iterations""", self.iteration_, self, Ediff, Dnorm)
psi4.driver.p4util.exceptions.SCFConvergenceError: Could not converge SCF iterations in 200 iterations.



ids :
{'53312391'}
-------------------------------------

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.2.3
openff.toolkit	0.10.0
basis_set_exchange	v0.8.13
qcelemental	v0.23.0
rdkit	2021.03.5

…M-post OpenFF Industry Benchmark Season 1 - MM v1.1

OpenFF Industry Benchmark Season 1 - MM v1.1

8778e73

dotsdl requested a review from jthorton July 30, 2021 14:51

dotsdl requested a review from pavankum August 6, 2021 15:26

Added environment file for MM submission

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pavankum approved these changes Aug 10, 2021

View reviewed changes

Added missing click pin to environment for industry benchmark MM subm…

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…ission

jthorton approved these changes Aug 11, 2021

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Added openff-2.0.0-rc.2 spec to MM industry benchmark dataset

96f0a99

dotsdl added the tracking label Aug 13, 2021

openff-dangerbot added this to Backlog in Dataset Tracking Aug 13, 2021

dotsdl added 2 commits August 13, 2021 10:08

Updated README index for MM industry benchmark dataset

24cb055

Added openff-forcefields >= 2.0.0-rc.2 to lifecycle and validation envs

3d3c07a

dotsdl merged commit 728ef71 into master Aug 13, 2021

Dataset Tracking automation moved this from Backlog to Queued for Submission Aug 13, 2021

openff-dangerbot moved this from Queued for Submission to Error Cycling in Dataset Tracking Aug 14, 2021

dotsdl added the priority-high label Aug 14, 2021

dotsdl moved this from Error Cycling to Requires Scientific Review in Dataset Tracking Aug 19, 2021

dotsdl moved this from Requires Scientific Review to Error Cycling in Dataset Tracking Sep 10, 2021

dotsdl added the compute-openff label Sep 14, 2021

dotsdl moved this from Error Cycling to End of Life in Dataset Tracking Oct 8, 2021

dotsdl removed the tracking label Dec 7, 2021

dotsdl added a commit that referenced this pull request Feb 23, 2022

Merge pull request #218 from openforcefield/industry-benchmark-v1.1-M…

3df7d81

…M-post OpenFF Industry Benchmark Season 1 - MM v1.1

dotsdl deleted the industry-benchmark-v1.1-MM-post branch February 23, 2022 17:37

OpenFF Industry Benchmark Season 1 - MM v1.1 #218

OpenFF Industry Benchmark Season 1 - MM v1.1 #218

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dotsdl commented Jul 30, 2021 • edited

New Submission Checklist

dotsdl commented Jul 30, 2021

openff-dangerbot commented Jul 30, 2021

QCSubmit Validation Report

QC Specification Report

pavankum commented Aug 8, 2021

dotsdl commented Aug 9, 2021

j-wags commented Aug 9, 2021 • edited

openff-dangerbot commented Aug 9, 2021

QCSubmit Validation Report

QC Specification Report

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dotsdl commented Aug 10, 2021 • edited

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QCSubmit Validation Report

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openff-dangerbot commented Aug 13, 2021

QCSubmit Validation Report

QC Specification Report

openff-dangerbot commented Aug 14, 2021

Lifecycle - QCSubmit Submission Report : SUCCESS

openff-dangerbot commented Aug 15, 2021

Lifecycle - Error Cycling Report

OptimizationRecord current status

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Lifecycle - Error Cycling Report

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openff-dangerbot commented Aug 17, 2021

Lifecycle - Error Cycling Report

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openff-dangerbot commented Sep 14, 2021

Lifecycle - Error Cycling Report

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Lifecycle - Error Cycling Report

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openff-dangerbot commented Sep 16, 2021

Lifecycle - Error Cycling Report

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openff-dangerbot commented Sep 22, 2021

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Lifecycle - Error Cycling Report

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openff-dangerbot commented Sep 26, 2021

Lifecycle - Error Cycling Report

dotsdl commented Jul 30, 2021 •

edited

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edited

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edited

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