Ferrocene derivative ligands fail

[rjrich]

DynamicBind jobs fail for ligands that are ferrocene derivatives. Apparently, RDKit cannot read the molecule. Here is the output from the terminal:

Read data/prepared_for_esm_HsAChE_5dh_chi_mol2.fasta with 1 sequences
Processing 1 of 1 batches (1 sequences)
Reading molecules and generating local structures with RDKit
0it [00:00, ?it/s]Explicit valence for atom # 0 C, 6, is greater than permitted
RDKit was unable to read the molecule.
Failed to read molecule /home/rjrich/DynamicBind/5dh_chi.mol2 We are skipping it. The reason is the exception: ('RDKit could not read the molecule ', '/home/rjrich/DynamicBind/5dh_chi.mol2')
1it [00:00, 1395.31it/s]
Reading language model embeddings.
Generating graphs for ligands and proteins
loading complexes: 0it [00:00, ?it/s]
loading data from memory: data/cache_torsion/limit0_INDEX_maxLigSizeNone_H0_recRad15.0_recMax24_esmEmbeddings3706429492/heterographs.pkl
Number of complexes: 0
Traceback (most recent call last):
File "/home/rjrich/DynamicBind/inference.py", line 138, in
test_dataset = PDBBind(transform=None, root='', name_list=name_list, protein_path_list=protein_path_list, ligand_descriptions=ligand_descriptions,
File "/home/rjrich/DynamicBind/datasets/pdbbind.py", line 157, in init
print_statistics(self.complex_graphs)
File "/home/rjrich/DynamicBind/datasets/pdbbind.py", line 781, in print_statistics
print(f"{name[i]}: mean {np.mean(array)}, std {np.std(array)}, max {np.max(array)}")
File "<array_function internals>", line 200, in amax
File "/home/rjrich/anaconda3/envs/dynamicbind/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 2820, in amax
return _wrapreduction(a, np.maximum, 'max', axis, None, out,
File "/home/rjrich/anaconda3/envs/dynamicbind/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation maximum which has no identity
inference complete.

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Is there a way to format a ligand file for ferrocene derivatives that will enable DynamicBind to accept the ligand?