# RNA-RNA docking with modified nucleotides

**URL:** <https://ask.bioexcel.eu/t/rna-rna-docking-with-modified-nucleotides/577>\
**Category:** HADDOCK\
**Created:** [October 28, 2017, 1:19pm UTC](https://ask.bioexcel.eu/t/rna-rna-docking-with-modified-nucleotides/577 "2017-10-28T13:19:58Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Hemant\_Arya](https://avatars.discourse-cdn.com/v4/letter/h/fbc32d/32.png) [@Hemant\_Arya](https://ask.bioexcel.eu/u/Hemant_Arya)\
**Post date:** [October 28, 2017, 1:19pm UTC](https://ask.bioexcel.eu/t/rna-rna-docking-with-modified-nucleotides/577/1 "2017-10-28T13:19:58Z")

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Dear HADDOCK admins and users,

I want to perform RNA-RNA docking using Haddock server. I have a mRNA structure that I would like to dock with a tRNA structure.

I modified uracil (atom level modification) but while running it shows an error message

“Second pdb file contains multiple residues with number 34 in chain A”  
Suggest me how can I proceed.

Thanks in advance.

Kind regards,  
Hemant

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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:** [October 28, 2017, 1:55pm UTC](https://ask.bioexcel.eu/t/rna-rna-docking-with-modified-nucleotides/577/2 "2017-10-28T13:55:20Z")

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Renumber your PDB - make sure you don’t have duplicated atom names in the same residue

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**Author:** ![Hemant\_Arya](https://avatars.discourse-cdn.com/v4/letter/h/fbc32d/32.png) [@Hemant\_Arya](https://ask.bioexcel.eu/u/Hemant_Arya)\
**Post date:** [November 2, 2017, 2:06pm UTC](https://ask.bioexcel.eu/t/rna-rna-docking-with-modified-nucleotides/577/3 "2017-11-02T14:06:10Z")

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Thank You 🙂 🙂 It works.