# Protein-Ligand docking error

**URL:** <https://ask.bioexcel.eu/t/protein-ligand-docking-error/3997>\
**Category:** HADDOCK\
**Created:** [November 16, 2022, 12:54pm UTC](https://ask.bioexcel.eu/t/protein-ligand-docking-error/3997 "2022-11-16T12:54:35Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![chris](https://avatars.discourse-cdn.com/v4/letter/c/958977/32.png) [@chris](https://ask.bioexcel.eu/u/chris)\
**Post date:** [November 16, 2022, 12:54pm UTC](https://ask.bioexcel.eu/t/protein-ligand-docking-error/3997/1 "2022-11-16T12:54:35Z")

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Good evening and sorry for the inconvenience,

I am trying to dock a protein and a ligand with HADDOCK 2.4, but when I put the pdb file of the ligand, I get the following error:

Error in PDB file.  
Issue when parsing the PDB file at line **1**.  
Residue number must be an integer (is ’ ')

Here’s a sample of the starting point of the aformentioned pdb file:

 ![Στιγμιότυπο οθόνης (32)](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/1a48f981eceef4efe3959cab5460f9f28de79b7d.png)

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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 16, 2022, 3:36pm UTC](https://ask.bioexcel.eu/t/protein-ligand-docking-error/3997/2 "2022-11-16T15:36:57Z")

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All atom names must be unique…

I.e. either generate your ligand with some other software (e.g. RDKit - check our shape-restraint ligand docking protocol on [bonvinlab.org/education](http://bonvinlab.org/education)) or manually edit the PDB file and add for example a number to each atom type (C1, C2, C3…) to make them unique.