"MissingParameterError" at torsion_optimisation stage #374
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I use gfn2xtb method in qc_options and gaff2 forcefield in parametrisation. |
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Hello,
I'm using qubekit to do some testing work. The program stopped at the "torsion_optimisation" stage.
The input molecule is a glycine.
I ran the following command:
qubekit run -i mol.sdf -n mol -c config.json -s hessian -s charges -s virtual_sites -s non_bonded -s bonded_parameters -s optimisationI tried many times and it always stopped with a "MissingParameterError"
Error
Torsiondrive finished and QM results saved. Performing torsion optimisations using ForceBalance. Traceback (most recent call last): File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/qubekit/workflow/workflow.py", line 335, in _run_stage result_mol = stage.run( File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/qubekit/torsions/fitting/forcebalance_wrapper.py", line 274, in run return self._optimise(molecule=molecule) File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/qubekit/torsions/fitting/forcebalance_wrapper.py", line 309, in _optimise self.generate_forcefield(molecule=molecule) File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/qubekit/torsions/fitting/forcebalance_wrapper.py", line 353, in generate_forcefield master_parameter = copy_mol.TorsionForce[master_dihedral] File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/qubekit/forcefield/force_groups.py", line 48, in __getitem__ raise MissingParameterError qubekit.utils.exceptions.MissingParameterErrorThe above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/user/anaconda3/envs/qubekit/bin/qubekit", line 10, in
sys.exit(cli())
File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/qubekit/cli/run.py", line 135, in run
workflow.new_workflow(molecule=molecule, skip_stages=skip_stages, end=end)
File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/qubekit/workflow/workflow.py", line 257, in new_workflow
return self._run_workflow(
File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/qubekit/workflow/workflow.py", line 295, in _run_workflow
molecule = self._run_stage(
File "/home/user/anaconda3/envs/qubekit/lib/python3.8/site-packages/qubekit/workflow/workflow.py", line 359, in _run_stage
raise WorkFlowExecutionError(
qubekit.utils.exceptions.WorkFlowExecutionError: The workflow stopped unexpectedly due to the following error at stage: torsion_optimisation
Then I checked that
__getitem__in force_groups.py. But I have no idea why theitem(4, 0, 1, 2) (correspongding to (5,1,2,3) in the graph) can not be found in theparameter. Much appreciate for your help.Here is my environment:
conda list
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