# Antibody numbering

**URL:** <https://ask.bioexcel.eu/t/antibody-numbering/4329>\
**Category:** HADDOCK\
**Created:** [May 22, 2023, 7:47am UTC](https://ask.bioexcel.eu/t/antibody-numbering/4329 "2023-05-22T07:47:18Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![iwurh](https://avatars.discourse-cdn.com/v4/letter/i/cc9497/32.png) [@iwurh](https://ask.bioexcel.eu/u/iwurh)\
**Post date:** [May 22, 2023, 7:47am UTC](https://ask.bioexcel.eu/t/antibody-numbering/4329/1 "2023-05-22T07:47:18Z")

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There is a problem with the pdb file because of the numbering used (IMGT) for the antibodies. The IMGT numbering puts in our pdb file annotations like 111 and 111A and this puts an error message:  
Error in PDB file. Your PDB contains multiple residues with number 111 in chain H or duplicated atom names.

How can I avoid this error message?

Thanks for your help

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**Author:** ![marco.giulini](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco.giulini/32/961_2.png) [@marco.giulini](https://ask.bioexcel.eu/u/marco.giulini)\
**Post date:** [May 22, 2023, 8:05am UTC](https://ask.bioexcel.eu/t/antibody-numbering/4329/2 "2023-05-22T08:05:43Z")

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Hi,

IMGT numbering is not compatible with HADDOCK: it is better to renumber the antibody residues so that 111A becomes 112 and so on. One way to do this is by means of pdb-tools ([pdb-tools/pdbtools at master · haddocking/pdb-tools · GitHub](https://github.com/haddocking/pdb-tools/tree/master/pdbtools) , web-portal [PDB-Tools Web](https://wenmr.science.uu.nl/pdbtools/)) and in particular pdb\_reres. For a detailed tutorial of docking antibodies with HADDOCK please check the following [HADDOCK2.4 Antibody - Antigen tutorial using PDB-tools webserver – Bonvin Lab](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/#using-pdb-tools-to-renumber-the-antibody-and-to-extract-the-variable-domain-fv)

Cheers

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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:** [May 22, 2023, 8:48am UTC](https://ask.bioexcel.eu/t/antibody-numbering/4329/3 "2023-05-22T08:48:28Z")

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Another tutorial describing how to do it (command line) using our pdb-tools:

> **[Antibody-antigen modelling tutorial using a local version of HADDOCK3](https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen/#preparing-pdb-files-for-docking)**
>
> A tutorial describing the use of HADDOCK3 to model an antibody-antigen complex

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**Author:** ![iwurh](https://avatars.discourse-cdn.com/v4/letter/i/cc9497/32.png) [@iwurh](https://ask.bioexcel.eu/u/iwurh)\
**Post date:** [May 22, 2023, 11:00am UTC](https://ask.bioexcel.eu/t/antibody-numbering/4329/4 "2023-05-22T11:00:22Z")

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Thank you for your answers