UNOFFICIAL
I'm finding that if I run packmol-memgen using pdb2pqr it's crashing after being unable to access a temp file from RCSB. If I use --reduce to avoid pdb2pqr everything works, and when running pdb2pqr directly I don't have problems either. The name of the file changes every time, though always starts with tmp so I assume pdb2pqr inside packmol is trying to download something it needs, but I'm not clear why.
Error message is:
Traceback (most recent call last):
File "/home/craig/miniconda3/envs/AmberTools26/bin/pdb2pqr30", line 10, in <module>
sys.exit(main())
^^^^^^
File "/home/craig/miniconda3/envs/AmberTools26/lib/python3.12/site-packages/pdb2pqr/main.py", line 829, in main
if main_driver(args) == 1:
^^^^^^^^^^^^^^^^^
File "/home/craig/miniconda3/envs/AmberTools26/lib/python3.12/site-packages/pdb2pqr/main.py", line 766, in main_driver
pdblist, is_cif = io.get_molecule(args.input_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/craig/miniconda3/envs/AmberTools26/lib/python3.12/site-packages/pdb2pqr/io.py", line 453, in get_molecule
input_file = get_pdb_file(input_path)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/craig/miniconda3/envs/AmberTools26/lib/python3.12/site-packages/pdb2pqr/io.py", line 438, in get_pdb_file
raise IOError(errstr)
OSError: Got code 404 while retrieving https://files.rcsb.org/download/tmpwtnak15e.pdb
Dr Craig Morton (he/him)
Drug Discovery Lead | Chemical Biology and Botanicals | Biotherapeutics | CSIRO
Innovative Bioproduction Platforms Theme Lead | Advanced Engineering Biology FSP
E Craig.Morton.csiro.au<mailto:Craig.Morton.csiro.au> | W
https://research.csiro.au/biotherapeutics/
A Ian Wark Laboratories, Bayview Ave, Clayton, VIC 3168, Australia
T +61 3 95185991
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Received on Mon Jul 20 2026 - 20:30:02 PDT
