# How to run prodigy to calculate the energy of a complex

**URL:** <https://ask.bioexcel.eu/t/how-to-run-prodigy-to-calculate-the-energy-of-a-complex/4947>\
**Category:** PRODIGY\
**Created:** [April 27, 2024, 12:42am UTC](https://ask.bioexcel.eu/t/how-to-run-prodigy-to-calculate-the-energy-of-a-complex/4947 "2024-04-27T00:42:48Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![zhangl](https://avatars.discourse-cdn.com/v4/letter/z/9dc877/32.png) [@zhangl](https://ask.bioexcel.eu/u/zhangl)\
**Post date:** [April 27, 2024, 12:42am UTC](https://ask.bioexcel.eu/t/how-to-run-prodigy-to-calculate-the-energy-of-a-complex/4947/1 "2024-04-27T00:42:48Z")

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I have a protein dimer (chain A and B) in which those two proteins were connected with a disulfide bond. I want to calculate the energy of this complex. I am wondering if prodigy can do that? If yes, how to select the chains in interactor 1 and interactor 2? Thank you.

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**Author:** ![zhangl](https://avatars.discourse-cdn.com/v4/letter/z/9dc877/32.png) [@zhangl](https://ask.bioexcel.eu/u/zhangl)\
**Post date:** [April 27, 2024, 12:47am UTC](https://ask.bioexcel.eu/t/how-to-run-prodigy-to-calculate-the-energy-of-a-complex/4947/2 "2024-04-27T00:47:16Z")

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I had the error message from the prodigy as shown below.

## PRODIGY\_590572

[+] Reading structure file: /data/runs/590572/protein-ref-2.pdb  
[+] Parsed structure file protein-ref-2 (2 chains, 214 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: 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/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:** [April 28, 2024, 2:58pm UTC](https://ask.bioexcel.eu/t/how-to-run-prodigy-to-calculate-the-energy-of-a-complex/4947/3 "2024-04-28T14:58:28Z")

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IUPAC naming of ILE is CD1 and not CD…