INFO:PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO:Checking and transforming input arguments.
INFO:Loading topology files.
INFO:Loading molecule: HA15.box.pdb
ERROR:Error parsing line: invalid literal for int() with base 10: ''
ERROR:<REMARK    THIS IS A SIMULATION BOX>
ERROR:Truncating remaining errors for record type:REMARK
WARNING:Warning: HA15.box.pdb is a non-standard PDB file.

ERROR:['REMARK']
INFO:Dropping water from structure.
INFO:Setting up molecule.
WARNING:Unable to find amino or nucleic acid definition for BGL.  Parsing as new residue.
WARNING:Unable to find amino or nucleic acid definition for BGL.  Parsing as new residue.
WARNING:Unable to find amino or nucleic acid definition for BGL.  Parsing as new residue.
WARNING:Unable to find amino or nucleic acid definition for BGL.  Parsing as new residue.
WARNING:Unable to find amino or nucleic acid definition for BGL.  Parsing as new residue.
WARNING:Unable to find amino or nucleic acid definition for BGL.  Parsing as new residue.
WARNING:Unable to find amino or nucleic acid definition for BGL.  Parsing as new residue.
WARNING:Unable to find amino or nucleic acid definition for BGL.  Parsing as new residue.
WARNING:Unable to find amino or nucleic acid definition for BGL.  Parsing as new residue.
WARNING:Suppressing further "Unable to find amino or nucleic acid definition for" messages
INFO:Created biomolecule object with 30 residues and 693 atoms.
INFO:Setting termini states for biomolecule chains.
INFO:Loading forcefield.
INFO:Loading hydrogen topology definitions.
CRITICAL:No biomolecule heavy atoms found and no ligand present. Unable to proceed.  You may also see this message if PDB2PQR does not have parameters for any residue in your biomolecule.
CRITICAL:Giving up.
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/main.py", line 792, in main_driver
    results = non_trivial(
  File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/main.py", line 617, in non_trivial
    if is_repairable(biomolecule, args.ligand is not None):
  File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/main.py", line 450, in is_repairable
    raise ValueError(err)
ValueError: No biomolecule heavy atoms found and no ligand present. Unable to proceed.  You may also see this message if PDB2PQR does not have parameters for any residue in your biomolecule.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/bin/pdb2pqr30", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/main.py", line 829, in main
    if main_driver(args) == 1:
  File "/usr/local/lib/python3.8/dist-packages/pdb2pqr/main.py", line 802, in main_driver
    raise RuntimeError from err
RuntimeError