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Describe the bug I tried to run 2D torsion scan but failed.
To Reproduce
import numpy as np from openff.toolkit import Molecule, ForceField import qcengine from qcelemental.models.procedures import TorsionDriveInput, TDKeywords, QCInputSpecification, OptimizationSpecification # load the molecule lig = Molecule.from_file('lig_ejm_55.sdf') # load the combined bespokefit force field ff = ForceField('combined.offxml') # now make the scan job torsion_task = TorsionDriveInput( keywords=TDKeywords( dihedrals=[(4, 10, 16, 12), (4, 7, 15, 11)], grid_spacing=[15,15] ), initial_molecule=[ lig.to_qcschema() ], input_specification=QCInputSpecification( model={'method': 'combined.offxml', 'basis': 'smirnoff'}, ), optimization_spec=OptimizationSpecification( procedure='geometric', keywords={ 'program': 'openmm', 'coordsys': 'dlc', 'enforce': 0.1, 'reset': True, 'qccnv': True, 'epsilon': 0.0 } ) ) result = qcengine.compute_procedure(torsion_task, 'torsiondrive', raise_error=True) with open('combined_2D_scan.json', 'w') as output: output.write(result.json())
Expected behavior It runs.
Additional context I got the error
Traceback (most recent call last): File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 3550, in run_code exec(code_obj, self.user_global_ns, self.user_ns) File "<ipython-input-2-3991d0bf5926>", line 1, in <module> runfile('/Users/zwu/Desktop/Torsion/openff/run_torsion_drive.py', wdir='/Users/zwu/Desktop/Torsion/openff') File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_umd.py", line 197, in runfile pydev_imports.execfile(filename, global_vars, local_vars) # execute the script ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile exec(compile(contents+"\n", file, 'exec'), glob, loc) File "/Users/zwu/Desktop/Torsion/openff/run_torsion_drive.py", line 41, in <module> result = qcengine.compute_procedure(torsion_task, 'torsiondrive', raise_error=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/compute.py", line 179, in compute_procedure output_data = executor.compute(input_data, config) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 138, in compute output_data = self._compute(input_model, config) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 70, in _compute grid_point_results = self._spawn_optimizations(next_jobs=next_jobs, input_model=input_model, config=config) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 228, in _spawn_optimizations grid_point_results = { ^ File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 229, in <dictcomp> grid_point: [self._spawn_optimization(grid_point, job, input_model, config) for job in jobs] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 229, in <listcomp> grid_point: [self._spawn_optimization(grid_point, job, input_model, config) for job in jobs] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 189, in _spawn_optimization "set": [ ^ File "/Users/zwu/mambaforge/envs/danny/lib/python3.11/site-packages/qcengine/procedures/torsiondrive.py", line 193, in <listcomp> "value": int(angle), ^^^^^^^^^^ ValueError: invalid literal for int() with base 10: '15,180'
I think one should change https://github.com/MolSSI/QCEngine/blob/master/qcengine/procedures/torsiondrive.py#L184 to angles = grid_point.split(',') lig_ejm_55.sdf.zip
angles = grid_point.split(',')
The text was updated successfully, but these errors were encountered:
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Describe the bug
I tried to run 2D torsion scan but failed.
To Reproduce
Expected behavior
It runs.
Additional context
I got the error
I think one should change
https://github.com/MolSSI/QCEngine/blob/master/qcengine/procedures/torsiondrive.py#L184
to
angles = grid_point.split(',')
lig_ejm_55.sdf.zip
The text was updated successfully, but these errors were encountered: