Two errors in minimal redundant network with Kartograph Mapper

AntoniaRabe commented 1 week ago

I tried to calculate an edge that does not have a perfect mapping and got two error messages. Can you please explain the meaning behind them? What exactly is the issue here?

0_easy_rbfe_A_complex_B_complex … Done with all simulations! Analyzing the results.... Here is the result: dG = None ± None Error: The protocol unit 'A - lig to B - lig repeat 2 generation 0' failed with the error message: IndexError: list index out of range
1_easy_rbfe_A_solvent_B_solvent … Parameterizing molecules [13:46:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 16 17 Done with all simulations! Analyzing the results.... Here is the result: dG = None ± None Error: The protocol unit 'A - lig to B - lig repeat 2 generation 0' failed with the error message: ValueError: Cannot construct openff.toolkit.topology.Molecule from <rdkit.Chem.rdchem.Mol object at 0x7f27f50919a0> No registered toolkits can provide the capability "from_object" for args "(<rdkit.Chem.rdchem.Mol object at 0x7f27f50919a0>,)" and kwargs "{'allow_undefined_stereo': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"

IAlibay commented 4 days ago

@AntoniaRabe are there more error outputs you can provide?

Also can you confirm what versions of OpenFE, rdkit, and openff-toolkit you are using?

IAlibay commented 4 days ago

From an initial look, it seems like your input molecules are incorrectly defined.

AntoniaRabe commented 3 days ago

Hello Mr. Alibay,

thank you for the quick response.

Versions: openfe 1.0.1 openff-toolkit 0.15.2

rdkit 2023.03.3

My calculations are with SMN2 ligands. Two ligands don't seem to fit the binding pose from the crystal structure: 8CF2 and 8R63 that's why I anticipated a high rmsd or an error already. I just don't really know the specifics of the error. For the other ligands, e.g. 8R62, everything went fine.

For the two calculations all the files are attached.

Thanks for your help.

BR, Antonia

Antonia Rabe B. Sc. BMC Masterstudent @ CzodrowskiLab

Johannes Gutenberg University Mainz Department of Chemistry Institute of Physical Chemistry Duesbergweg 10-14 55128 Mainz

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Von: Irfan Alibay @.***> Gesendet: Samstag, 5. Oktober 2024 15:53:49 An: OpenFreeEnergy/openfe Cc: Rabe, Antonia Marie; Mention Betreff: Re: [OpenFreeEnergy/openfe] Two errors in minimal redundant network with Kartograph Mapper (Issue #948)

From an initial look, it seems like your input molecules are incorrectly defined.

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OpenFreeEnergy / openfe

Two errors in minimal redundant network with Kartograph Mapper #948