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

PRODIGY
1

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

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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

2

The correct PDB nomenclature for ILE atom CD is: CD1

If you change it it might work :slight_smile:

3

Thanks for reaching out about this issue.

The error you are seeing;

[!] 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.