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Torsion scan unit nanometer vs nanometer**2 #80

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pbute opened this issue Oct 15, 2021 · 0 comments
Open

Torsion scan unit nanometer vs nanometer**2 #80

pbute opened this issue Oct 15, 2021 · 0 comments

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@pbute
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pbute commented Oct 15, 2021

Hi, I'm currently doing a torsion scan to improve the dihedrals of some molecules but I'm getting an error regarding the units of the position of the coordinates. I've tried a couple of approaches to fix the problem because the code was working with an earlier release in April or May. I'm currently trying to fix the issue using a diphenylmethane but I haven't been successful. Any input as to what the issue maybe would be useful. Below I pasted the error that I'm getting. Thanks!!

BFGS: 60 09:36:31 -13673.084137 0.0124
BFGS: 61 09:36:31 -13673.084155 0.0096

TypeError Traceback (most recent call last)
/ipykernel_22881/1791874995.py in
14 mol, paramol_settings, amber_symmetrizer = generate_fresh_system(mol_name)
15 torsion_scan = TorsionScan()
---> 16 torsion_scan.run_task(paramol_settings,
17 [mol],
18 [torsion_to_scan],

python3.8/site-packages/ParaMol/Tasks/torsions_scan.py in run_task(self, settings, systems, torsions_to_scan, scan_settings, interface, torsions_to_freeze, ase_constraints, optimize_qm, optimize_qm_before_scan, optimize_mm, optimize_mm_before_scan, optimize_mm_type, sampling, rotate_from_initial, n_structures_to_sample, dihedral_conservation_threshold, mm_opt_force_constant, mm_opt_tolerance, mm_opt_max_iter, rdkit_conf, restart)
170 if torsional_scan_dim == 1:
171 # Perform 1D Scan
--> 172 scan_angles, qm_energies_list, qm_forces_list, qm_conformations_list, mm_energies_list, mm_conformations_list = self.scan_1d(
173 interface, settings.restart, system, conf, torsions_to_scan[0], torsions_to_freeze, scan_settings[0], optimize_qm, optimize_qm_before_scan,
174 optimize_mm, optimize_mm_before_scan, optimize_mm_type, ase_constraints, sampling, rotate_from_initial, n_structures_to_sample, dihedral_conservation_threshold,

python3.8/site-packages/ParaMol/Tasks/torsions_scan.py in scan_1d(self, interface, restart_settings, system, rdkit_conf, torsion_to_scan, torsions_to_freeze, scan_settings, optimize_qm, optimize_qm_before_scan, optimize_mm, optimize_mm_before_scan, optimize_mm_type, ase_constraints, sampling, rotate_from_initial, n_structures_to_sample, threshold, mm_opt_force_constant, mm_opt_tolerance, mm_opt_max_iter, restart)
468
469 # Set positions of context to last position
--> 470 dummy_context.setPositions(positions * unit.nanometers)
471
472 # Set RDKit geometry to the current in the OpenMM context

python3.8/site-packages/openmm/openmm.py in setPositions(self, positions)
3676
3677 if unit.is_quantity(positions):
-> 3678 positions = positions.value_in_unit(unit.nanometer)
3679
3680

python3.8/site-packages/openmm/unit/quantity.py in value_in_unit(self, unit)
621 Returns underlying value, in the specified units.
622 """
--> 623 val = self.in_units_of(unit)
624 if is_quantity(val):
625 return val._value

python3.8/site-packages/openmm/unit/quantity.py in in_units_of(self, other_unit)
657 """
658 if not self.unit.is_compatible(other_unit):
--> 659 raise TypeError('Unit "%s" is not compatible with Unit "%s".' % (self.unit, other_unit))
660 f = self.unit.conversion_factor_to(other_unit)
661 return self._change_units_with_factor(other_unit, f)

TypeError: Unit "nanometer**2" is not compatible with Unit "nanometer".

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