Comments (2)
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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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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Related Issues (20)
- Abnormal memory usage in protocaller HOT 13
- Can I use ProtoCaller in protein-protein system? HOT 4
- The merge has opened/closed a ring HOT 12
- An input file contains a line longer than 4095 characters HOT 4
- LINCS warning and structure clash HOT 7
- Can I supply a ligand coordinate file as input? HOT 1
- H bond constraint HOT 1
- How to supply a custom pdb file (without pdb id) for protein? HOT 2
- Memory usage constantly growing with the number of perturbations. HOT 6
- Select chain from polymer HOT 5
- Molecule ID not found HOT 1
- Explicit valence for atom # 37 C greater than permitted HOT 5
- Error while calling command 'antechamber' HOT 1
- minimise not take effect when protonated was set to True HOT 2
- Invalid file format for file HOT 2
- tleap failed for protein HOT 2
- Not all chains are contained in the FASTA sequence
- Installing error
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