How to run prodigy to calculate the energy of a complex

PRODIGY
1

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.

2

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

3

IUPAC naming of ILE is CD1 and not CD…