# Using Zn2 as a ligand

**URL:** <https://ask.bioexcel.eu/t/using-zn2-as-a-ligand/1302>\
**Category:** HADDOCK\
**Created:** [November 29, 2018, 10:42pm UTC](https://ask.bioexcel.eu/t/using-zn2-as-a-ligand/1302 "2018-11-29T22:42:35Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![lfrench](https://avatars.discourse-cdn.com/v4/letter/l/fbc32d/32.png) [@lfrench](https://ask.bioexcel.eu/u/lfrench)\
**Post date:** [November 29, 2018, 10:42pm UTC](https://ask.bioexcel.eu/t/using-zn2-as-a-ligand/1302/1 "2018-11-29T22:42:35Z")

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Dear Prof.Bonvin and coworkers  
I am interested in study protein-Zn interaction using HADDOCK server: the Easy interface. I use this file as a PDB for Zn.  
HETATM 1 ZN+2 ZN2 1 1.603 11.925 27.136 0.50 31.56 ZN  
END  
However I received an email with the following error:  
“There was an inconsistency in your data  
Error message  
First pdb file is incorrectly formatted. Please align the columns of your PDB properly.”

I tried to do it some times but it doens’t work. Would you help me to fix this file or suggest me what should I do, please?,  
Thanks you

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**Author:** ![Adrimel](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adrimel/32/40_2.png) [@Adrimel](https://ask.bioexcel.eu/u/Adrimel)\
**Post date:** [November 30, 2018, 8:13am UTC](https://ask.bioexcel.eu/t/using-zn2-as-a-ligand/1302/2 "2018-11-30T08:13:39Z")

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To check if there are some formatting issues (the PDB format is character-based), you can use `pdb_format.py` from our set of [pdb-tools](https://github.com/haddocking/pdb-tools)

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**Author:** ![joaor](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/joaor/32/194_2.png) [@joaor](https://ask.bioexcel.eu/u/joaor)\
**Post date:** [November 30, 2018, 8:48am UTC](https://ask.bioexcel.eu/t/using-zn2-as-a-ligand/1302/3 "2018-11-30T08:48:32Z")

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The PDB format is quite strict with spacing and it’s very easy to make mistakes editing it manually. As Adrien suggested, have a look at our pdb-tools. We just released a new version and some tools changed name: pdb\_validate is now the tool to check where a structure is badly formatted.

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**Author:** ![lfrench](https://avatars.discourse-cdn.com/v4/letter/l/fbc32d/32.png) [@lfrench](https://ask.bioexcel.eu/u/lfrench)\
**Post date:** [November 30, 2018, 8:56pm UTC](https://ask.bioexcel.eu/t/using-zn2-as-a-ligand/1302/4 "2018-11-30T20:56:27Z")

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The problem was resolved using the pdb-tools.  
Thanks you very much.