Getting CRITICAL:Found gap in biomolecule structure for atom

[Tonylac77]

Thanks a lot for the work done here.

I am trying to generate .pdbqt files using Meeko (https://github.com/forlilab/Meeko) and was recommended to use PDB2PQR to parse the PDB files before reading into Meeko as PDB2PQR converts the HIS residue naming (at least for the AMBER format)

I've been trying to get this to run on a few test files, without success.

2024-05-21 21:14:30,627 CRITICAL:main.py:809:main_driver:Found gap in biomolecule structure for atom ATOM    657 HOE2 GLU    40     -23.146 191.664 125.495  0.0000 0.0000
2024-05-21 21:14:30,627 CRITICAL:main.py:810:main_driver:Giving up.

I have attached the .log file and some examples files I have tried this one, all giving the same error.

Here's the code to reproduce :

if input_format == "pdb" and output_format == "pdbqt":
        try:
            # Run the pdb2pqr command
            subprocess.call(
                f"pdb2pqr --ff=AMBER --ffout=AMBER --keep-chain --nodebump {input_file} {input_file.with_suffix('.pqr')} -q",
                shell=True,
                stdout=subprocess.DEVNULL,
                stderr=subprocess.DEVNULL)
            # Run the mk_prepare_receptor.py script
            subprocess.call(
                f"{dockm8_path}/scripts/utilities/mk_prepare_receptor.py --pdb {input_file.with_suffix('.pqr')} -o {output_file} --skip_gpf",
                shell=True,
                stdout=subprocess.DEVNULL,
                stderr=subprocess.DEVNULL)
            os.remove(input_file.with_suffix(".pqr")) if os.path.exists(input_file.with_suffix(".pqr")) else None
            return output_file

1fvv_p.zip