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msuruzhon avatar msuruzhon commented on June 11, 2024 1

This must be an issue with how RDKit sanitises SMILES strings, I think that's one of the reasons why SDF files should be preferred. An AMBER mol2 file will never work with RDKit because it's not actually a valid mol2 file (it's more like a parameter file, much like GROMACS top), it's just called like that for historical reasons.

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kexul avatar kexul commented on June 11, 2024

I tried use the generated ligand1_protonated.pdb file and ligand1_protonated.sdf, which produce no error. But, when I used the ligand1_protonated_antechamber.mol2 as input, another error occurred:

****
Post-condition Violation
Element 'o' not found
Violation occurred on line 91 in file /home/conda/feedstock_root/build_artifacts/rdkit_1578668820522/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****

/data/FEP/prepare/ProtoCaller/Wrappers/rdkitwrapper.py:189: UserWarning: No template containing bond information was supplied. Resulting geometry might be wrong
  _warnings.warn("No template containing bond information was supplied. "
Traceback (most recent call last):
  File "/root/repo/prepare/teth_validate.py", line 184, in <module>
    lig = Ligand('ligand1_protonated_antechamber.mol2', protonated=True, minimise=False, workdir='test_case', parametrised_files=['ligand1.prmtop', 'ligand1.inpcrd'])
  File "/data/FEP/prepare/ProtoCaller/Ensemble/Ligand.py", line 56, in __init__
    template=input)
  File "/data/FEP/prepare/ProtoCaller/Wrappers/rdkitwrapper.py", line 194, in openAsRdkit
    mol = AssignBondOrdersFromTemplate(template, mol)
  File "/data/FEP/prepare/ProtoCaller/Wrappers/rdkitwrapper.py", line 282, in AssignBondOrdersFromTemplate
    atom1 = match[b.GetBeginAtomIdx()]
KeyError: 7

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