PRODIGY Error running my PDB file containing my docked proteins from ClusPro

PRODIGY
22

Hello Sir,

After changing ILE, atom: CD should be CD1

I also have issues with the PRODIGY error running my PDB file.

PRODIGY_709173

[+] Reading structure file: /data/runs/709173/trj_20.pdb
[+] Parsed structure file trj_20 (4 chains, 1625 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 584, in freesasa.structureFromBioPDB
File “src/structure.pyx”, line 214, in freesasa.Structure.setRadiiWithClassifier
File “src/structure.pyx”, line 235, in freesasa.Structure.setRadii
AssertionError: Error: Radius is <= 0 (-1.0) for the residue: CYS, atom: OT1

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

23

Read the error message: next atom naming problem:

CYS, atom: OT1 - should be simply O and OT2 should be OXT

24

Dear Sir,
There is some error detected when I run the protein-peptide complex for the calculation of the ‘Kd value.’

PRODIGY_1179912

Error: # =========================================================================== command: prodigy Pep11-HSA-Kd Final.pdb --selection A B --temperature 25 --contact_list --pymol_selection exit status: 1 log:

25

Is this the full log file?

26

Yes, Sir. I have tried many times, but this type of result came.

27

without the full log file we can’t help you

Most likely an issue with your input PDB file…