# Radius array is \<= 0 for the residue: ASP ,atom: OT1

**URL:** <https://ask.bioexcel.eu/t/radius-array-is-0-for-the-residue-asp-atom-ot1/4793>\
**Category:** Uncategorized\
**Created:** [February 6, 2024, 11:22am UTC](https://ask.bioexcel.eu/t/radius-array-is-0-for-the-residue-asp-atom-ot1/4793 "2024-02-06T11:22:06Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ARUN](https://avatars.discourse-cdn.com/v4/letter/a/ee7513/32.png) [@ARUN](https://ask.bioexcel.eu/u/ARUN)\
**Post date:** [February 6, 2024, 11:22am UTC](https://ask.bioexcel.eu/t/radius-array-is-0-for-the-residue-asp-atom-ot1/4793/1 "2024-02-06T11:22:06Z")

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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.

# ===========================================================================

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

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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:** [February 6, 2024, 11:51am UTC](https://ask.bioexcel.eu/t/radius-array-is-0-for-the-residue-asp-atom-ot1/4793/2 "2024-02-06T11:51:13Z")

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> 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.

OT1 is not a standard PDB atom name - you should convert your OT1/OT2 to O/OXT