openff-toolkit: Unable to assign all BCCs in mol - switch to `setPermissiveBCCs` to fall back to AM1 when no BCC available

Describe the bug Many molecules in the coverage set are not able to be loaded, probably because the AN1BCC model has missing types.

To Reproduce Files: report.tar.gz

Output

$ python reproduce.py 
Warning: BCIChargeCorrector: BCI charge corrections for mol 
Warning:                     missing bcc parameter for the O3-O5 bond (BCIType 310931)
Warning: OEBCCPartialCharges: Unable to assign all BCCs in mol 
Warning: OESEmpBCCPartialCharges: Stopping the charging process at the first stage for mol 
Traceback (most recent call last):
  File "reproduce.py", line 10, in <module>
    system = forcefield.create_openmm_system(topology)
  File "/home/qyd/codes/anaconda3/envs/openff/lib/python3.7/site-packages/openforcefield/typing/engines/smirnoff/forcefield.py", line 1139, in create_openmm_system
    parameter_handler.create_force(system, topology, **kwargs)
  File "/home/qyd/codes/anaconda3/envs/openff/lib/python3.7/site-packages/openforcefield/typing/engines/smirnoff/parameters.py", line 2466, in create_force
    temp_mol.compute_partial_charges_am1bcc(toolkit_registry=toolkit_registry)
  File "/home/qyd/codes/anaconda3/envs/openff/lib/python3.7/site-packages/openforcefield/topology/molecule.py", line 2014, in compute_partial_charges_am1bcc
    self
  File "/home/qyd/codes/anaconda3/envs/openff/lib/python3.7/site-packages/openforcefield/utils/toolkits.py", line 3006, in call
    return method(*args, **kwargs)
  File "/home/qyd/codes/anaconda3/envs/openff/lib/python3.7/site-packages/openforcefield/utils/toolkits.py", line 1258, in compute_partial_charges_am1bcc
    raise Exception('Unable to assign charges')
Exception: Unable to assign charges

Computing environment (please complete the following information):

  • Operating system: Ubuntu 16.04
  • Output of running conda list conda_list.txt

Additional context For this molecule, the O-O bond is causing the error if I understand correctly. However, many other molecules also have errors when loading. Do we want to fix them one by one or there is a better way to fix them all?

Screenshot for the reported molecule: image

About this issue

  • Original URL
  • State: closed
  • Created 5 years ago
  • Comments: 22 (20 by maintainers)

Most upvoted comments

But… we may have to ask support about this, because it’s an option to OEAM1BCCCharges but we’re doing ELF10 charges, which is a composite of engines. Chris suggests e-mailing support. I’ll e-mail support.