# Protein DNA run fails

**URL:** <https://ask.bioexcel.eu/t/protein-dna-run-fails/1065>\
**Category:** HADDOCK\
**Created:** [July 16, 2018, 7:18am UTC](https://ask.bioexcel.eu/t/protein-dna-run-fails/1065 "2018-07-16T07:18:06Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![diffracteD](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)\
**Post date:** [July 16, 2018, 7:18am UTC](https://ask.bioexcel.eu/t/protein-dna-run-fails/1065/1 "2018-07-16T07:18:06Z")

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Hi,  
I’m trying to dock a 20 bp DNA with a Protein. I have prepared the DNA from haddock dna modelling server and trying to dock it with a multimeric protein’s crystal structure.  
However, the docking fails repeatedly saying “First pdb file contains multiple chains with overlapping numbering: A5 - B5”

Is it not possible to run docking with multiple chain containing protein ?  
Please help me out here. I’m keeping the protein and DNA file here [https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0](https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)

Thank you.

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**Author:** ![mtrellet](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/mtrellet/32/42_2.png) [@mtrellet](https://ask.bioexcel.eu/u/mtrellet)\
**Post date:** [July 16, 2018, 12:35pm UTC](https://ask.bioexcel.eu/t/protein-dna-run-fails/1065/2 "2018-07-16T12:35:37Z")

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Hello,

This is possible to provide a PDB with multiple chains but then you need to have unique residue IDs for all residues. Meaning that your second chain (here `B`) should start with residue ID 202 (last residue ID from chain `A` + 1).

Mikael

PS: Note that this forum is searchable and the answer to your question is already provided… E.g.:

> [@Dealing with dimers](http://ask.bioexcel.eu/t/dealing-with-dimers/42):
>
> Hellow everybody I have problems using Haddock for dimers. I’ve received several different messages: Using pdb (from pdb databse) There was an inconsistency in your data Error message First pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble using a pdb with only one chain (but is a dimer) There was an inconsistency in your data Error message First pdb file contai…

and

> [@Error in the docking process (overlapping numbering)](http://ask.bioexcel.eu/t/error-in-the-docking-process-overlapping-numbering/963):
>
> Hi! I received a email with this error: There was an inconsistency in your data Error message First pdb file contains multiple chains with overlapping numbering: A151 - B151 How can I solve it? Thanks!