Can't kekulize mol. Unkekulized atoms: 5 8 9

[gsuchunli]

When I ran the test using the scripts from the paper "AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization", I got the following error:

Start time at: 2025-04-15 04:03:49.914840
End time at: 2025-04-15 04:04:00.250176
Total time at: 0:00:10.335336
[04:04:36] Can't kekulize mol. Unkekulized atoms: 5 8 9
[04:04:36] Can't kekulize mol. Unkekulized atoms: 5 8 9
Traceback (most recent call last):
File "", line 198, in _run_module_as_main
File "", line 88, in _run_code
File "/home/sunil/anaconda3/lib/python3.11/site-packages/mpi4py/main.py", line 7, in
main()
File "/home/sunil/anaconda3/lib/python3.11/site-packages/mpi4py/run.py", line 214, in main
run_command_line(args)
File "/home/sunil/anaconda3/lib/python3.11/site-packages/mpi4py/run.py", line 46, in run_command_line
run_path(sys.argv[0], run_name='main')
File "", line 291, in run_path
File "", line 98, in _run_module_code
File "", line 88, in _run_code
File "/home/sunil/Downloads/autogrow4/run_autogrow.py", line 87, in
main()
File "/home/sunil/Downloads/autogrow4/run_autogrow.py", line 66, in main
AutogrowMainExecute.main_execute(user_vars)
File "/home/sunil/Downloads/autogrow4/autogrow/autogrow_main_execute.py", line 107, in main_execute
smile_file_new_gen, new_gen_ligands_list = operations.populate_generation(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sunil/Downloads/autogrow4/autogrow/operators/operations.py", line 362, in populate_generation
conversion_to_3d.convert_to_3d(vars, smiles_to_convert_file, new_gen_folder_path)
File "/home/sunil/Downloads/autogrow4/autogrow/operators/convert_files/conversion_to_3d.py", line 92, in convert_to_3d
gypsum_output_folder_path = convert_smi_to_sdfs_with_gypsum(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sunil/Downloads/autogrow4/autogrow/operators/convert_files/conversion_to_3d.py", line 167, in convert_smi_to_sdfs_with_gypsum
failed_to_convert = vars["parallelizer"].run(job_input, run_gypsum_multiprocessing)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sunil/Downloads/autogrow4/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Parallelizer.py", line 327, in run
return self.parallel_obj.run(func, args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sunil/Downloads/autogrow4/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Parallelizer.py", line 593, in run
result_chunk = [func(*arg) for arg in args_chunk]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sunil/Downloads/autogrow4/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Parallelizer.py", line 593, in
result_chunk = [func(*arg) for arg in args_chunk]
^^^^^^^^^^
File "/home/sunil/Downloads/autogrow4/autogrow/operators/convert_files/conversion_to_3d.py", line 343, in run_gypsum_multiprocessing
did_gypsum_complete = check_gypsum_log_did_complete(log_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sunil/Downloads/autogrow4/autogrow/operators/convert_files/conversion_to_3d.py", line 379, in check_gypsum_log_did_complete
data = log.readlines()
^^^^^^^^^^^^^^^
File "", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode bytes in position 821-822: invalid continuation byte
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

My input was below:

{
"filename_of_receptor": "/home/sunil/chunli/prmt5/fragment/tutorial/PARP/4r6eA_PARP1_prepared.pdb",
"center_x": -70.76,
"center_y": 21.82,
"center_z": 28.33,
"size_x": 25.0,
"size_y": 16.0,
"size_z": 25.0,
"source_compound_file": "/home/sunil/chunli/prmt5/fragment/tutorial/source_compounds/Fragment_MW_100_to_150.smi",
"root_output_folder": "/home/sunil/chunli/prmt5/fragment/tutorial/out/out2",
"conversion_choice": "MGLToolsConversion",
"mgltools_directory": "/home/sunil/Downloads/mgltools_x86_64Linux2_1.5.6/",
"prepare_ligand4.py": "/home/sunil/Downloads/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py",
"prepare_receptor4.py": "/home/sunil/Downloads/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py",
"mgl_python": "/home/sunil/Downloads/mgltools_x86_64Linux2_1.5.6/bin/pythonsh",
"number_of_mutants_first_generation": 500,
"number_of_crossovers_first_generation": 500,
"number_elitism_advance_from_previous_gen_first_generation": 40,
"number_of_mutants": 2500,
"number_of_crossovers": 2500,
"number_elitism_advance_from_previous_gen": 500,
"top_mols_to_seed_next_generation_first_generation": 50,
"top_mols_to_seed_next_generation": 500,
"diversity_mols_to_seed_first_generation": 500,
"diversity_seed_depreciation_per_gen": 5,
"num_generations": 30,
"number_of_processors": 16,
"dock_choice": "QuickVina2Docking",
"scoring_choice": "VINA",
"selector_choice": "Rank_Selector",
"LipinskiStrictFilter": true,
"GhoseFilter": true,
"PAINSFilter": true,
"reduce_files_sizes": true,
"max_variants_per_compound": 5,
"filter_source_compounds": false,
"use_docked_source_compounds": true,
"rxn_library": "all_rxns",
"multithread_mode": "mpi",
"start_a_new_run": true
}

Thanks,