# Prodigy fails to calculate binding energy of protein-protein complex

**URL:** <https://ask.bioexcel.eu/t/prodigy-fails-to-calculate-binding-energy-of-protein-protein-complex/3420>\
**Category:** Uncategorized\
**Created:** [January 20, 2022, 10:26am UTC](https://ask.bioexcel.eu/t/prodigy-fails-to-calculate-binding-energy-of-protein-protein-complex/3420 "2022-01-20T10:26:30Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![usharma](https://avatars.discourse-cdn.com/v4/letter/u/57b2e6/32.png) [@usharma](https://ask.bioexcel.eu/u/usharma)\
**Post date:** [January 20, 2022, 10:26am UTC](https://ask.bioexcel.eu/t/prodigy-fails-to-calculate-binding-energy-of-protein-protein-complex/3420/1 "2022-01-20T10:26:30Z")

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in the two chain protein complex docked structure (protein1-A, Protein B), prodigy fails with following message

**tatus: Failed**

Your run failed. Please find below the output of your run which might include an indication about why your run failed :

[!] Structure contains gaps:  
A ALA1 \< Fragment 0 \> A GLY73  
A GLY75 \< Fragment 1 \> A GLU133  
A GLN135 \< Fragment 2 \> A TYR170  
A GLY174 \< Fragment 3 \> A ALA201  
B SER24 \< Fragment 4 \> B CYS281

Running Prodigy for structure BMP1-Szl-complex1  
ERROR:  
[!] Error when running freesasa:  
[!] Error: Radius array is \<= 0 for the residue: ILE ,atom: CD

Please anyone can suggest me how the issue can be rectified.

many thanks,

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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:** [January 20, 2022, 11:02am UTC](https://ask.bioexcel.eu/t/prodigy-fails-to-calculate-binding-energy-of-protein-protein-complex/3420/2 "2022-01-20T11:02:01Z")

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The nomenclature of the ILE atoms is not correct: CD should be CD1 (if I am correct…)

Official PDB namings

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<div class="post-metadata">

**Author:** ![usharma](https://avatars.discourse-cdn.com/v4/letter/u/57b2e6/32.png) [@usharma](https://ask.bioexcel.eu/u/usharma)\
**Post date:** [January 20, 2022, 11:32am UTC](https://ask.bioexcel.eu/t/prodigy-fails-to-calculate-binding-energy-of-protein-protein-complex/3420/3 "2022-01-20T11:32:10Z")

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is there a way to fix such errors by some program. After fixing ILE CD now I am getting error due to Ala OT1. These pdbs are generated from MD simulation trajectory?

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**Author:** ![joaomcteixeira](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/joaomcteixeira/32/480_2.png) [@joaomcteixeira](https://ask.bioexcel.eu/u/joaomcteixeira)\
**Post date:** [January 26, 2022, 9:29am UTC](https://ask.bioexcel.eu/t/prodigy-fails-to-calculate-binding-energy-of-protein-protein-complex/3420/4 "2022-01-26T09:29:57Z")

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Dear @usharma

We have developed a tool within our `pdb-tools` package to rename atom names across the different atom name nomenclatures in PDB files. Yet, this tool is under review and is not yet part of the official `pdb-tools` package. If you are skilled with GitHub you can see [the PR here](https://github.com/haddocking/pdb-tools/pull/114).

Otherwise, for now, you can rename the `OT1` name to `O ` using any of your favourite text editors (not Word, but pure text). Please mind that `O ` is followed by two spaced to compensate for the `T1`. It is likely you will need to modify `OT2` also to `OXT`.

Asap, we integrate our new tool in `pdb-tools` package we will let you know. If you don’t know `pdb-tools` please visit → [http://www.bonvinlab.org/pdb-tools/](http://www.bonvinlab.org/pdb-tools/)

Cheers,  
João T