OpenFreeEnergy / OpenFreeEnergy/openfe

Transformation between oxo- ,-thio -seleno groups

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#278 5 comments 0 reactions 1 assignee View on GitHub

@dwhswenson is already working on this.

Since Apr 17, 2023.

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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:
image

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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