# How to revert back the docked PDB residue number to original residue number

**URL:** <https://ask.bioexcel.eu/t/how-to-revert-back-the-docked-pdb-residue-number-to-original-residue-number/648>\
**Category:** HADDOCK\
**Created:** [November 30, 2017, 6:53am UTC](https://ask.bioexcel.eu/t/how-to-revert-back-the-docked-pdb-residue-number-to-original-residue-number/648 "2017-11-30T06:53:01Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\
**Post date:** [November 30, 2017, 6:53am UTC](https://ask.bioexcel.eu/t/how-to-revert-back-the-docked-pdb-residue-number-to-original-residue-number/648/1 "2017-11-30T06:53:01Z")

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The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [http://www.bonvinlab.org/software/haddock2.2](http://www.bonvinlab.org/software/haddock2.2)

Hi, i need to ask how to convert the residue number of docked PDB back to original residue number while keeping the ligand interaction?

This is because i changed the residue number of dimer protein to avoid overlapping in residue number using pdb-tools when preparing the receptor PDB for docking.

Would appreciate if anyone can kindly explain.

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**Author:** ![Andrea\_Spitaleri](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/andrea_spitaleri/32/37_2.png) [@Andrea\_Spitaleri](https://ask.bioexcel.eu/u/Andrea_Spitaleri)\
**Post date:** [November 30, 2017, 7:31am UTC](https://ask.bioexcel.eu/t/how-to-revert-back-the-docked-pdb-residue-number-to-original-residue-number/648/2 "2017-11-30T07:31:26Z")

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Hi, if it is just one pdb file have look here:

> **[mmagnus/emacs-pdb-mode](https://github.com/mmagnus/emacs-pdb-mode)**
>
> pdb-mode is an emacs-lisp minor mode for Emacs to perform a number of useful editing functions on Protein DataBank (PDB) formatted files. XEmacs and/or GNU Emacs are available for most computing pl...

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**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\
**Post date:** [November 30, 2017, 12:51pm UTC](https://ask.bioexcel.eu/t/how-to-revert-back-the-docked-pdb-residue-number-to-original-residue-number/648/3 "2017-11-30T12:51:03Z")

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Thanks for the suggestion.

I would like to know if the ligand-protein interaction will become inaccurate after the modification? It is because i got different interaction result after modification of PDB using pdb-tool master.

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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:** [November 30, 2017, 1:45pm UTC](https://ask.bioexcel.eu/t/how-to-revert-back-the-docked-pdb-residue-number-to-original-residue-number/648/4 "2017-11-30T13:45:34Z")

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This kind of computations has a chaotic character. You are not ensure to get exactly the same results depending on where your jobs has run.

In principle renumbering a molecule will not affect the coordinates and thus the results. But if you define active/passive residues make sure to also correct the numbering of those.

Which is why it is important to not consider only one models, but analysis several within a cluster and also look at several of the top ranking clusters.