Problem with a complex file from cluspro when trying to used PRODIGY

PRODIGY
1

I get this error when I tried to run PRODIGY with a comple from cluspro. Please help me!!# ===========================================================================
command: /usr/local/bin/prodigy output_1_1.pdb --selection A F --temperature 25.0 --contact_list --pymol_selection
exit status: 1
log:
[+] Reading structure file: /data/runs/pcm_3SMtsbYu/output_1_1.pdb
[+] Parsed structure file output_1_1 (2 chains, 364 residues)
Traceback (most recent call last):
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/freesasa_tools.py”, line 207, in execute_freesasa_api
struct = structureFromBioPDB(
File “src/structure.pyx”, line 510, in freesasa.structureFromBioPDB
File “src/structure.pyx”, line 187, in freesasa.Structure.setRadiiWithClassifier
File “src/structure.pyx”, line 208, in freesasa.Structure.setRadii
AssertionError: Error: Radius array is <= 0 for the residue: HIS ,atom: OD

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/usr/local/bin/prodigy”, line 8, in
sys.exit(main())
File “/usr/local/lib/python3.10/site-packages/prodigy/predict_IC.py”, line 421, in main
prodigy.predict(
File “/usr/local/lib/python3.10/site-packages/prodigy/predict_IC.py”, line 161, in predict
_, cmplx_sasa = execute_freesasa_api(self.structure)
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/freesasa_tools.py”, line 213, in execute_freesasa_api
error_message = “” + os.linesep()
TypeError: ‘str’ object is not callable

2

There is no OD atom in a Histidine…

PRODIGY expects standard atom names and the error actually comes from freesasa which does not know how to handle a OD atom for an HIS.