# Error: Radius array is \<= 0 for the residue: ILE ,atom: CD

**URL:** <https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835>\
**Category:** PRODIGY\
**Created:** [March 7, 2021, 9:42pm UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835 "2021-03-07T21:42:39Z")\
**Posts on this page:** 10\
**Page:** 1

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**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://ask.bioexcel.eu/u/lanselibai)\
**Post date:** [March 7, 2021, 9:42pm UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/1 "2021-03-07T21:42:39Z")

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I got this error message when submitting a PDB:

```
Running Prodigy for structure md_0_1_noPBC
ERROR:
[!] Error when running freesasa:
[!] Error: Radius array is <= 0 for the residue: ILE ,atom: CD

```

It seems that [someone else has similar error previously](https://github.com/haddocking/prodigy/issues/12).

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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:** [March 8, 2021, 8:01am UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/2 "2021-03-08T08:01:01Z")

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The proper atom name should be rather `CD1` instead of `CD` for ILE.

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**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://ask.bioexcel.eu/u/lanselibai)\
**Post date:** [March 8, 2021, 10:24am UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/3 "2021-03-08T10:24:21Z")

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Thank you. I have changed the `CD` to `CD1` for `ILE`.

I also have `OT1` and `OT2` atoms at the C termini, which causes the same problem `Error: Radius array is <= 0 for the residue`. How should I modify them?

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<div class="post-metadata">

**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:** [March 8, 2021, 10:48am UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/4 "2021-03-08T10:48:53Z")

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Standard PBD naming (freesasa relies on that and is not our software). I.e. `O` and `OXT`

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<div class="post-metadata">

**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://ask.bioexcel.eu/u/lanselibai)\
**Post date:** [March 8, 2021, 11:24am UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/5 "2021-03-08T11:24:55Z")

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Thank you! It works now!

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<div class="post-metadata">

**Author:** ![aghdam](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@aghdam](https://ask.bioexcel.eu/u/aghdam)\
**Post date:** [February 4, 2023, 6:05pm UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/6 "2023-02-04T18:05:01Z")

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what about this error?!

_Running Prodigy for structure gsk3b2\_complexfit\_24_  
_ERROR:_  
_[!] Error when running freesasa:_  
_[!] Error: Radius array is \<= 0 for the residue: HIS ,atom: O1P_

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<div class="post-metadata">

**Author:** ![aghdam](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@aghdam](https://ask.bioexcel.eu/u/aghdam)\
**Post date:** [February 4, 2023, 6:17pm UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/7 "2023-02-04T18:17:18Z")

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and even O2P and O3P

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<div class="post-metadata">

**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 4, 2023, 7:12pm UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/8 "2023-02-04T19:12:24Z")

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These simply do not belong to a histidine amino acid. Prodigy does not support modified amino acids

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<div class="post-metadata">

**Author:** ![aghdam](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@aghdam](https://ask.bioexcel.eu/u/aghdam)\
**Post date:** [February 4, 2023, 8:30pm UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/9 "2023-02-04T20:30:21Z")

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then what can I do about this?  
how should I replace them that doesn’t harm the structure?

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<div class="post-metadata">

**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 5, 2023, 2:34pm UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835/10 "2023-02-05T14:34:58Z")

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Again modified amino acids are not supported.

You can delete the phosphate to get some binding affinity estimates, but it will not be the same molecule