ValueError - name of the atom is not in list

[kirmedvedev]

I am generating phosphorylated SER in different proteins. In the majority of cases everything is fine, however in some cases I got this error:
///
Running PSIPRED'
Running hhsearch
Using the cif atom ordering for TRP.
./make_msa.sh /project/biophysics/Nick_lab/s171179/ecod_drugbank/rosetta_runs/fasta/P07711.fasta P07711_DB03661_OCS_SER_142_OG_Phosphorylation/A 4 64 pdb100_2021Mar03/pdb100_2021Mar03
Error executing job with overrides: []
Traceback (most recent call last):
File "/project/biophysics/Nick_lab/s171179/drugbank/soft/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 208, in main
runner.infer()
File "/project/biophysics/Nick_lab/s171179/drugbank/soft/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 154, in infer
self.parse_inference_config()
File "/project/biophysics/Nick_lab/s171179/drugbank/soft/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 69, in parse_inference_config
covalent_sm_inputs, residues_to_atomize_covale = load_covalent_molecules(protein_inputs, self.config, self)
File "/project/biophysics/Nick_lab/s171179/drugbank/soft/RoseTTAFold-All-Atom/rf2aa/data/covale.py", line 40, in load_covalent_molecules
residues_to_atomize, combined_molecules, extra_bonds = find_residues_to_atomize(protein_inputs, sm_inputs, covalent_bonds, model_runner)
File "/project/biophysics/Nick_lab/s171179/drugbank/soft/RoseTTAFold-All-Atom/rf2aa/data/covale.py", line 81, in find_residues_to_atomize
file, atom_index = convert_residue_to_molecule(protein_inputs, residue, model_runner)
File "/project/biophysics/Nick_lab/s171179/drugbank/soft/RoseTTAFold-All-Atom/rf2aa/data/covale.py", line 125, in convert_residue_to_molecule
atom_index = atom_names.index(atom_to_bond.strip())
ValueError: 'OG' is not in list
Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.
///
I don't understand the difference between the cases. Why sometime it does not work? Any ideas?
Thank you!