# Prodigy Error: Radius array is \<= 0 for the residue: ILE ,atom: CD

**URL:** <https://ask.bioexcel.eu/t/prodigy-error-radius-array-is-0-for-the-residue-ile-atom-cd/4375>\
**Category:** PRODIGY\
**Created:** [June 10, 2023, 9:54pm UTC](https://ask.bioexcel.eu/t/prodigy-error-radius-array-is-0-for-the-residue-ile-atom-cd/4375 "2023-06-10T21:54:31Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![waldo.acevedo](https://avatars.discourse-cdn.com/v4/letter/w/71e660/32.png) [@waldo.acevedo](https://ask.bioexcel.eu/u/waldo.acevedo)\
**Post date:** [June 10, 2023, 9:54pm UTC](https://ask.bioexcel.eu/t/prodigy-error-radius-array-is-0-for-the-residue-ile-atom-cd/4375/1 "2023-06-10T21:54:31Z")

</div>

Please, anyone, help me to fix my run failed ( see below)?

# ===========================================================================

command: /usr/local/bin/prodigy neuroplastin\_peptide\_c.pdb --selection A B --temperature 25.0 --contact\_list --pymol\_selection  
exit status: 1  
log:  
[+] Reading structure file: /data/runs/3Rq8BgFF/neuroplastin\_peptide\_c.pdb  
[+] Parsed structure file neuroplastin\_peptide\_c (2 chains, 1190 residues)

[!] Error when running freesasa:  
[!] Error: Radius array is \<= 0 for the residue: ILE ,atom: CD  
Traceback (most recent call last):  
File “/usr/local/lib/python3.10/dist-packages/prodigy/lib/freesasa\_tools.py”, line 194, 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: ILE ,atom: CD

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/dist-packages/prodigy/predict\_IC.py”, line 389, in main  
prodigy.predict(  
File “/usr/local/lib/python3.10/dist-packages/prodigy/predict\_IC.py”, line 159, in predict  
\_, cmplx\_sasa = execute\_freesasa\_api(self.structure)  
File “/usr/local/lib/python3.10/dist-packages/prodigy/lib/freesasa\_tools.py”, line 202, in execute\_freesasa\_api  
raise Exception(error\_message)  
Exception:  
[!] Error when running freesasa:  
[!] Error: Radius array is \<= 0 for the residue: ILE ,atom: CD

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<div class="post-metadata">

**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:** [June 11, 2023, 11:01am UTC](https://ask.bioexcel.eu/t/prodigy-error-radius-array-is-0-for-the-residue-ile-atom-cd/4375/2 "2023-06-11T11:01:39Z")

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The correct PDB nomenclature for ILE atom CD is: CD1

If you change it it might work 🙂

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**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [June 12, 2023, 7:05am UTC](https://ask.bioexcel.eu/t/prodigy-error-radius-array-is-0-for-the-residue-ile-atom-cd/4375/3 "2023-06-12T07:05:31Z")

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Thanks for reaching out about this issue.

The error you are seeing;

```plaintext
[!] Error: Radius array is <= 0 for the residue: ILE ,atom: CD

```

Could be an indication that PRODIGY cannot find the `CD` atom of an Isoleucin in your input structure. Depending on how your input structure was generated, the atom `CD` from ILE could be named `CD1` - this is the case from structures coming from AMBER if I remember well.

To account for that you need to manually edit the input PDB file and replace the CD1 atoms with CD, which is the expected format for PRODIGY.