Parametrize moelcule with B atom possible?

[DaniDelHoyo]

I would like to know whether espaloma can be used to parametrize a molecule containing a Boron atom. I am guessing the answer is no, since I have tried it, but just in case I was doing something wrong. The concrete molecule is Bocillin (https://pubchem.ncbi.nlm.nih.gov/compound/52941401#section=2D-Structure).

[mikemhenry]

What error do you get? SPICE contains Boron
https://github.com/openmm/spice-dataset

[mikemhenry]

That said it might not support it, I would have to check the but the error you get will help since it might be supported but some other tooling doesn't support it.

[DaniDelHoyo]

Hi, thank you for answering. I am using it with OpenMM TemplateGenerators:

molecule = Molecule.from_file(sdfFile)
tempGen = EspalomaTemplateGenerator(molecules=molecule, forcefield='espaloma-0.3.2')
tempGen.generate_residue_template(molecule)

The complete error goes:

tempGenerator.generate_residue_template(molecule)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "openmm-8.1.2/lib/python3.11/site-packages/openmmforcefields/generators/template_generators.py", line 1975, in generate_residue_template
system = esp.graphs.deploy.openmm_system_from_graph(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "openmm-8.1.2/lib/python3.11/site-packages/espaloma/graphs/deploy.py", line 116, in openmm_system_from_graph
sys = ff.create_openmm_system(
^^^^^^^^^^^^^^^^^^^^^^^^
File "openmm-8.1.2/lib/python3.11/site-packages/openff/utilities/utilities.py", line 81, in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "openmm-8.1.2/lib/python3.11/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1164, in create_openmm_system
return self.create_interchange(
^^^^^^^^^^^^^^^^^^^^^^^^
File "openmm-8.1.2/lib/python3.11/site-packages/openff/utilities/utilities.py", line 81, in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "openmm-8.1.2/lib/python3.11/site-packages/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1223, in create_interchange
return Interchange.from_smirnoff(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "openmm-8.1.2/lib/python3.11/site-packages/openff/interchange/components/interchange.py", line 270, in from_smirnoff
return _create_interchange(
^^^^^^^^^^^^^^^^^^^^
File "openmm-8.1.2/lib/python3.11/site-packages/openff/interchange/smirnoff/_create.py", line 105, in _create_interchange
_bonds(interchange, force_field, _topology, partial_bond_orders_from_molecules)
File "openmm-8.1.2/lib/python3.11/site-packages/openff/interchange/smirnoff/_create.py", line 149, in _bonds
"Bonds": SMIRNOFFBondCollection.create(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "openmm-8.1.2/lib/python3.11/site-packages/openff/interchange/smirnoff/_valence.py", line 277, in create
handler.store_matches(parameter_handler=parameter_handler, topology=topology)
File "openmm-8.1.2/lib/python3.11/site-packages/openff/interchange/smirnoff/_valence.py", line 169, in store_matches
_check_all_valence_terms_assigned(
File "openmm-8.1.2/lib/python3.11/site-packages/openff/interchange/smirnoff/_base.py", line 180, in _check_all_valence_terms_assigned
raise exception
openff.interchange.exceptions.UnassignedBondError: BondHandler was not able to find parameters for the following valence terms:

Topology indices (33, 41): names and elements (B1 B), (F1 F),
Topology indices (33, 36): names and elements (B1 B), (N5 N),
Topology indices (33, 42): names and elements (B1 B), (F2 F),
Topology indices (30, 33): names and elements (N4 N), (B1 B),

[mattwthompson]

OpenFF mainline force fields to not support (read: have parameters for) Boron