Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Torsion scan unit nanometer vs nanometer**2 #80

Open
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

Comments

@pbute
Copy link

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".

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant