# Gap in protein chain and atom naming error

**URL:** <https://ask.bioexcel.eu/t/gap-in-protein-chain-and-atom-naming-error/3825>\
**Category:** PRODIGY\
**Created:** [July 27, 2022, 5:57pm UTC](https://ask.bioexcel.eu/t/gap-in-protein-chain-and-atom-naming-error/3825 "2022-07-27T17:57:18Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Gagan](https://avatars.discourse-cdn.com/v4/letter/g/5f9b8f/32.png) [@Gagan](https://ask.bioexcel.eu/u/Gagan)\
**Post date:** [July 27, 2022, 5:57pm UTC](https://ask.bioexcel.eu/t/gap-in-protein-chain-and-atom-naming-error/3825/1 "2022-07-27T17:57:18Z")

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Dear PRODIGY Team and Users,  
I am facing the following errors on my protein-protein complex when submitted for PRODIGY analysis. One of my interacting protein has some residues missing due to which i am receiving error and some atom naming errors also. Please let me know how to proceed further and what modifications are required

[!] Structure contains gaps:  
B GLY1 \< Fragment 0 \> B ASN219  
A VAL30 \< Fragment 1 \> A GLN336  
A LEU343 \< Fragment 2 \> A THR664

Running Prodigy for structure vaccine-A-TLR3-B  
ERROR:  
[!] Error when running freesasa:  
[!] Error: Radius array is \<= 0 for the residue: ILE ,atom: CD

Thanks in advance.

Best Regards,  
Gagandeep Singh

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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:** [July 27, 2022, 9:12pm UTC](https://ask.bioexcel.eu/t/gap-in-protein-chain-and-atom-naming-error/3825/2 "2022-07-27T21:12:05Z")

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The gaps are not the problem. Your atom naming is not consistent with official pdb namings. ILE CD should be CD1[here](https://ask.bioexcel.eu/email/unsubscribe/752cb3f96ccee72c8b776f8f845f1c11c8cf4767db2363c1025335a7edb3f377).