OpenFreeEnergy / OpenFreeEnergy/openfe
Transformation between oxo- ,-thio -seleno groups
Open
@dwhswenson is already working on this.
Since Apr 17, 2023.
- Dominant language
- Python
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Description
Hello,
Upon trying to run transformation of 4-methylbenzooxodiazol to seleno- or thio- derivative, script crashes yielding an error:
rbfe_transform = RelativeLigandProtocol(
settings=rbfe_settings
)
complex_dag = rbfe_transform.create(
stateA=sel_complex, stateB=s_complex,
mapping={'ligand': se_to_s},
)
solvent_dag = rbfe_transform.create(
stateA=sel_solvent, stateB=s_solvent,
mapping={'ligand': se_to_s},
)
list(complex_dag.protocol_units)
complex_unit = list(complex_dag.protocol_units)[0]
complex_unit.run(dry=True, verbose=True)
ValueError: Cannot construct openff.toolkit.topology.Molecule from
No registered toolkits can provide the capability "from_object" for args "(,)" and kwargs "{'allow_undefined_stereo': True, '_cls': }"
Available toolkits are: [ToolkitWrapper around The RDKit version 2022.09.1, ToolkitWrapper around AmberTools version 22.0, ToolkitWrapper around Built-in Toolkit version None]
ToolkitWrapper around The RDKit version 2022.09.1 : The OpenFF Toolkit does not currently support parsing molecules with S- and P-block radicals. Found 1 radical electrons on molecule [H]c1c([H])c2n[s]nc2c(C([H])([H])[H])c1[H].
However, there is no radical, as you can see from the SMILE and picture below:

Is it some kind of just due to presence of sulfur (and selenium, in other case)?
I plan to use ff14SB/tip3p/openff-2.0.0-rc.2, but it fails before any topology is being created.
Regards,
Rafal
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