Error on charge computation for Residue ACE A 0 in Protein 1U19

[yaideltg]

The protein can be obtained at https://www.rcsb.org/structure/1U19

I'm on Fedora 41 (Workstation Edition)

When I try the following command in the console: ~$ pdb2pqr --chain A --ff AMBER 1U19.pdb temp.pdb

I get the following error:

WARNING:Suppressing further "Skipped atom during water optimization" messages
INFO:Applying force field to biomolecule states.
WARNING:Residue ACE A 0 has non-integer charge: -0.3369 deviates by 0.3369 from integral, exceeding error tolerance 0.001.
WARNING:Residue ACE B 0 has non-integer charge: -0.3369 deviates by 0.3369 from integral, exceeding error tolerance 0.001.
WARNING:Residue ACE A 0 has non-integer charge: -0.3369 deviates by 0.3369 from integral, exceeding error tolerance 0.001
WARNING:Residue ACE B 0 has non-integer charge: -0.3369 deviates by 0.3369 from integral, exceeding error tolerance 0.001
CRITICAL:-10.6738 deviates by 0.32620000000000005 from integral, exceeding error tolerance 0.001
CRITICAL:Giving up.
Traceback (most recent call last):
File "/home/yaidel/codes/pyarmm/.venv/lib/python3.13/site-packages/pdb2pqr/main.py", line 803, in main_driver
results = non_trivial(
args=args,
...<3 lines>...
is_cif=is_cif,
)
File "/home/yaidel/codes/pyarmm/.venv/lib/python3.13/site-packages/pdb2pqr/main.py", line 717, in non_trivial
raise ValueError(charge_err)
ValueError: -10.6738 deviates by 0.32620000000000005 from integral, exceeding error tolerance 0.001

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

Traceback (most recent call last):
File "/home/yaidel/codes/pyarmm/.venv/bin/pdb2pqr", line 8, in
sys.exit(main())
~~~~^^
File "/home/yaidel/codes/pyarmm/.venv/lib/python3.13/site-packages/pdb2pqr/main.py", line 841, in main
if main_driver(args) == 1:
~~~~~~~~~~~^^^^^^
File "/home/yaidel/codes/pyarmm/.venv/lib/python3.13/site-packages/pdb2pqr/main.py", line 813, in main_driver
raise RuntimeError from err
RuntimeError