Comments (14)
entropybit
commented on June 18, 2024
1
Okay I have simply appended a zip of the entire results folder here:
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entropybit
commented on June 18, 2024
1
Thanks a lot, I did all of this and just submitted a job with the fresh install. Let's see if it works this time ^^.
If so I'll close it afterwards.
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entropybit
commented on June 18, 2024
1
I think you should really update your requirements.txt.
openmm should be in it I guess, and after doing what you just proposed it first failed with module not found chemper ^^'.
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entropybit
commented on June 18, 2024
1
To be continued:
qubekit.utils.exceptions.WorkFlowExecutionError: The workflow stopped unexpectedly
due to the following error at stage: torsion_optimisation
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entropybit
commented on June 18, 2024
1
Holy crap
the first time it worked, thanks a lot.
And don't worry about the delay, although I have to say I was very near to write something like "bump" here.
I will see if I produce new errors with my other molecules and if not I will close this.
Also I'll probably never touch that conda environment again until my research is done and possibly make a few copies of it ^^'.
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jthorton
commented on June 18, 2024
Hi @entropybit ,
The error reporting is not great at that stage so its not always clear what has happened, there should be within the optimisation folder a json file called result.json which should have more information could you post that here it should help diagnose what's gone wrong.
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entropybit
commented on June 18, 2024
Sure, I assume you meant workflow_result.json:
{
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"modified_date": "2023_03_07",
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],
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{
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{
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],
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"type": "RBProperTorsionForce",
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},
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"type": "RBImproperTorsionForce",
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},
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"type": "NonbondedForce",
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{
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"charge": 0.11669999999999998,
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],
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},
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"hessian": null,
"qm_scans": null,
"wbo": null
},
"results": {
"parametrisation": {
"stage": "OpenFF",
"stage_settings": {
"type": "OpenFF",
"force_field": "openff_unconstrained-1.3.0.offxml"
},
"status": "done",
"error": null
},
"optimisation": {
"stage": "Optimiser",
"stage_settings": {
"type": "Optimiser",
"pre_optimisation_method": "gfn2xtb",
"seed_conformers": 40,
"maxiter": 350,
"convergence_criteria": "GAU_TIGHT"
},
"status": "error",
"error": [
" File \"/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py\", line 335, in _run_stage\n result_mol = stage.run(\n",
" File \"/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/helper_stages.py\", line 144, in run\n return self._run_qm_opt(\n",
" File \"/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/helper_stages.py\", line 206, in _run_qm_opt\n raise GeometryOptimisationError(\n"
]
},
"hessian": {
"stage": "Hessian",
"stage_settings": {
"type": "Hessian"
},
"status": "waiting",
"error": null
},
"charges": {
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"stage_settings": {
"type": "DDECCharges",
"solvent_settings": {
"program": "gaussian",
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"epsilon": 4.0,
"volume_contour": 0.0004
},
"program": "gaussian",
"basis": null,
"method": null,
"td_settings": null,
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},
"status": "waiting",
"error": null
},
"virtual_sites": {
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"stage_settings": null,
"status": "skip",
"error": null
},
"non_bonded": {
"stage": "LennardJones612",
"stage_settings": {
"type": "LennardJones612",
"lj_on_polar_h": true,
"free_parameters": {
"H": {
"v_free": 7.6,
"b_free": 6.5,
"r_free": 1.738
},
"X": {
"v_free": 7.6,
"b_free": 6.5,
"r_free": 1.083
},
"C": {
"v_free": 34.4,
"b_free": 46.6,
"r_free": 2.008
},
"N": {
"v_free": 25.9,
"b_free": 24.2,
"r_free": 1.765
},
"O": {
"v_free": 22.1,
"b_free": 15.6,
"r_free": 1.499
}
},
"alpha": 1.0,
"beta": 0.0
},
"status": "waiting",
"error": null
},
"bonded_parameters": {
"stage": "ModSeminario",
"stage_settings": {
"type": "ModSeminario",
"vibrational_scaling": 1.0
},
"status": "waiting",
"error": null
},
"torsion_scanner": {
"stage": "TorsionScan1D",
"stage_settings": {
"type": "TorsionScan1D",
"special_torsions": [],
"default_scan_range": [
-165,
180
],
"avoided_torsions": [
{
"smirks": "[*:1]-[CH3:2]"
},
{
"smirks": "[*:1]-[NH2:2]"
}
],
"torsion_driver": {
"type": "torsiondriver",
"n_workers": 1,
"grid_spacing": 15,
"energy_decrease_thresh": null,
"energy_upper_limit": null,
"starting_conformations": 4
}
},
"status": "waiting",
"error": null
},
"torsion_optimisation": {
"stage": "ForceBalanceFitting",
"stage_settings": {
"type": "ForceBalanceFitting",
"penalty_type": "L1",
"job_type": "optimize",
"max_iterations": 10,
"convergence_step_criteria": 0.01,
"convergence_objective_criteria": 0.01,
"convergence_gradient_criteria": 0.01,
"n_criteria": 1,
"eig_lowerbound": 0.01,
"finite_difference_h": 0.01,
"penalty_additive": 0.1,
"constrain_charge": false,
"initial_trust_radius": -0.25,
"minimum_trust_radius": 0.05,
"error_tolerance": 1.0,
"adaptive_factor": 0.2,
"adaptive_damping": 1.0,
"normalize_weights": false,
"extras": {},
"priors": {
"Proper_k": 6.0
},
"targets": {
"TorsionProfile_OpenMM": {
"target_name": "TorsionProfile_OpenMM",
"description": "Relaxed energy and RMSD fitting for torsion drives only.",
"writelevel": 2,
"keywords": {
"pdb": "molecule.pdb",
"coords": "scan.xyz"
},
"openmm_platform": "Reference",
"energy_denom": 1.0,
"energy_upper": 10.0,
"attenuate": false,
"restrain_k": 1.0
}
}
},
"status": "waiting",
"error": null
}
}
}from qubekit.
jthorton
commented on June 18, 2024
No there should be an output from qcengine in a folder called optimisation, the json file should contain the raw output from the QM software.
from qubekit.
jthorton
commented on June 18, 2024
Thanks very much! It looks like our most recent version on conda-forge (2.1.1) is missing a fix to work with Gaussian16. Ill look into updating this but for now, it should work if you install the main branch from github. These commands should help
Remove qubekit only from conda
conda uninstall qubekit --force
clone github code
git clone https://github.com/qubekit/QUBEKit.git
move into package
cd QUBEKit
install package
pip install .
from qubekit.
jthorton
commented on June 18, 2024
Thanks for testing this out, it looks like our new fragmentation changes caused some issues, the main branch should now work provided you use a protocol that does not use virtual sites. If you do need v-sites you will need a specific branch of the openff-toolkit, the 10-x branch which you can install via pip or from github for now.
from qubekit.
entropybit
commented on June 18, 2024
Hmh, I did exactly that and after mistakenly uninstalling and installing qubekit again I had to do the following things
pip install click
pip install qcengine
pip install torsiondrive
pip install forcebalance
conda install ndcctools -c conda-forge
pip install xtb
XTB i installed after this
(qubekit) [b_mayer@logc0002 fabi_ligands]$ qubekit run -sm CO -n methanol
Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing
Traceback (most recent call last):
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/bin/qubekit", line 8, in <module>
sys.exit(cli())
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/cli/run.py", line 136, in run
workflow.new_workflow(molecule=molecule, skip_stages=skip_stages, end=end)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 272, in new_workflow
return self._run_workflow(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 294, in _run_workflow
self.validate_workflow(workflow=workflow, molecule=molecule)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 122, in validate_workflow
pre_spec.validate_specification()
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/utils/datastructures.py", line 151, in validate_specification
self.validate_program()
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/utils/datastructures.py", line 100, in validate_program
raise SpecificationError(
qubekit.utils.exceptions.SpecificationError: The program xtb is not available, available programs are {'gaussian', 'rdkit'}
Now it seems to me it is not using gaussian/g16 anymore.
But with xtb it also doesn't work ^^
(qubekit) [b_mayer@logc0002 fabi_ligands]$ qubekit run -sm CO -n methanol
Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing
If QUBEKit ever breaks or you would like to view timings and loads of other info, view the log file.
Our documentation (README.md) also contains help on handling the various commands for QUBEKit.
Fragmenting molecule using the WBOFragmenter
Traceback (most recent call last):
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 348, in _run_stage
result_mol = stage.run(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/fragmentation/wbo_fragmenter.py", line 71, in run
return self._run(molecule, *args, **kwargs)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/fragmentation/wbo_fragmenter.py", line 79, in _run
fragmentation_result = self.fragment(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/fragmenter/fragment.py", line 916, in fragment
result = self._fragment(molecule, target_bond_smarts)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/fragmenter/fragment.py", line 1012, in _fragment
molecule = assign_elf10_am1_bond_orders(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/fragmenter/chemi.py", line 41, in assign_elf10_am1_bond_orders
molecule = _generate_conformers(molecule, max_confs, rms_threshold)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/fragmenter/chemi.py", line 98, in _generate_conformers
canonical_molecule.generate_conformers(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/toolkit/topology/molecule.py", line 3030, in generate_conformers
return toolkit_registry.call(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/toolkit/utils/toolkit_registry.py", line 380, in call
raise ValueError(msg)
ValueError: No registered toolkits can provide the capability "generate_conformers" for args "(Molecule with name '' and SMILES '[H][O][C]([H])([H])[H]',)" and kwargs "{'n_conformers': 800, 'rms_cutoff': <Quantity(1.0, 'angstrom')>, 'clear_existing': True, 'make_carboxylic_acids_cis': True}"
Available toolkits are: [ToolkitWrapper around The RDKit version 2022.09.1, ToolkitWrapper around AmberTools version 22.0, ToolkitWrapper around Built-in Toolkit version None]
ToolkitWrapper around The RDKit version 2022.09.1 <class 'AttributeError'> : Neither Quantity object nor its magnitude (1.0) has attribute 'value_in_unit'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/bin/qubekit", line 8, in <module>
sys.exit(cli())
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/cli/run.py", line 136, in run
workflow.new_workflow(molecule=molecule, skip_stages=skip_stages, end=end)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 272, in new_workflow
return self._run_workflow(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 310, in _run_workflow
molecule = self._run_stage(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 372, in _run_stage
raise WorkFlowExecutionError(
qubekit.utils.exceptions.WorkFlowExecutionError: The workflow stopped unexpectedly due to the following error at stage: fragmentation
I have appended you an zip of the entire generated output folder again.
methanol3.zip
from qubekit.
jthorton
commented on June 18, 2024
Hi @entropybit sorry for the delay. For the first part, there is a pre-optimisation stage in the workflow which uses a cheaper method to hopefully speed up the full QM optimisation. By default, this runs xtb-GFN2 but can be set to something else like ANI2-x. For the second part it looks like when installing manually you picked up a newer version of the openff-fragmenter for now you will need openff-toolkit=0.10.7 and openff-fragmenter=0.1.2 we should have a new conda package soon which makes this easier.
from qubekit.
jthorton
commented on June 18, 2024
Fantastic glad it finally works thanks for sticking with it and helping me get these issues sorted out, feel free to tag me in any other issues or help so I pick it up faster!
from qubekit.
entropybit
commented on June 18, 2024
Hmh, well I got a similiar result for my molecule that doesn't have S in it as I wrote in the seconde issue.
This:
Warning (not error because allow_undefined_stereo=True): Unable to make OFFMol from RDMol: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom C (index 7)
Stereochemistry for atom 37 flipped from R to None
Stereochemistry for atom 37 flipped from R to S
If QUBEKit ever breaks or you would like to view timings and loads of other info, view the log file.
Our documentation (README.md) also contains help on handling the various commands for QUBEKit.
Fragmenting molecule using the WBOFragmenter
Traceback (most recent call last):
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 348, in _run_stage
result_mol = stage.run(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/fragmentation/wbo_fragmenter.py", line 71, in run
return self._run(molecule, *args, **kwargs)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/fragmentation/wbo_fragmenter.py", line 83, in _run
depict_fragmentation_result(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/fragmenter/depiction.py", line 307, in depict_fragmentation_result
depict_fragments(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/fragmenter/depiction.py", line 332, in depict_fragments
header_svg = _oe_render_parent(parent, [*fragments])
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/fragmenter/depiction.py", line 92, in _oe_render_parent
oe_parent = parent.to_openeye()
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/openff/toolkit/utils/base_wrapper.py", line 50, in wrapped_function
raise ToolkitUnavailableException(msg)
openff.toolkit.utils.exceptions.ToolkitUnavailableException: This function requires the OpenEye Toolkit toolkit
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/bin/qubekit", line 8, in <module>
sys.exit(cli())
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/cli/run.py", line 136, in run
workflow.new_workflow(molecule=molecule, skip_stages=skip_stages, end=end)
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 272, in new_workflow
return self._run_workflow(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 310, in _run_workflow
molecule = self._run_stage(
File "/work/scratch/b_mayer/miniconda3/envs/qubekit/lib/python3.10/site-packages/qubekit/workflow/workflow.py", line 372, in _run_stage
raise WorkFlowExecutionError(
qubekit.utils.exceptions.WorkFlowExecutionError: The workflow stopped unexpectedly due to the following error at stage: fragmentation
But I guess that doesn't really have to do with the original problem here and is more of a me using the method wrong thing ?
(Help required anyways but I guess I will close this here with this comment and wait for your reply in the other issue).
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Related Issues (20)
- Output XML file format HOT 2
- QM Optimisation fails HOT 3
- Got stuck in torsion_scanner HOT 8
- Phosphorous valency 3 works but valency 5 does not work HOT 1
- Parallelism HOT 4
- MissingRfreeError: The following elements have no reference Rfree values HOT 14
- Conflict between QUBEKit and psi4 in conda HOT 3
- Setting solvent dielectric in psi4 workflow HOT 2
- Pydantic and changes in python 3.10
- "MissingParameterError" at torsion_optimisation stage HOT 1
- Migrate to new Pydantic
- Update plugins to work with interchange HOT 1
- Segfault in force_constant_bond genexpr HOT 3
- openff toolkit API changes: ChemicalEnvironment in qubekit.torsions.utils
- requirements.txt: specify versions, missing openff
- unfixed error in conda repo, fixed in GitHub? HOT 1
- openff API changes: TopologyAtom
- DDEC with psi4, or rather psi4 -> wfx
- Free atom parameters
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