Hello everyone,
to check the binding energy of docked complex, I am using prodigy webserver which showed an error such as “Radius array is <= 0 for the residue: ASP ,atom: OT1”. What to do further please guide me. Note:- this docked complex is the final frame of md simulation by charmm36 forcefield by gromacs.
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command: /usr/local/bin/prodigy G23D_CDK4_FS_.pdb --selection A B --temperature 25.0 --contact_list --pymol_selection
exit status: 1
log:
[+] Reading structure file: /data/runs/3UrGM4Mg/G23D_CDK4_FS_.pdb
[+] Parsed structure file G23D_CDK4_FS_ (2 chains, 462 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: ASP ,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