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

**URL:** <https://ask.bioexcel.eu/t/problem-with-a-complex-file-from-cluspro-when-trying-to-used-prodigy/4551>\
**Category:** PRODIGY\
**Created:** [September 26, 2023, 4:38am UTC](https://ask.bioexcel.eu/t/problem-with-a-complex-file-from-cluspro-when-trying-to-used-prodigy/4551 "2023-09-26T04:38:00Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![L33ANN2021](https://avatars.discourse-cdn.com/v4/letter/l/c6cbf5/32.png) [@L33ANN2021](https://ask.bioexcel.eu/u/L33ANN2021)\
**Post date:** [September 26, 2023, 4:38am UTC](https://ask.bioexcel.eu/t/problem-with-a-complex-file-from-cluspro-when-trying-to-used-prodigy/4551/1 "2023-09-26T04:38:00Z")

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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

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [September 26, 2023, 7:51am UTC](https://ask.bioexcel.eu/t/problem-with-a-complex-file-from-cluspro-when-trying-to-used-prodigy/4551/2 "2023-09-26T07:51:47Z")

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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.