# Error in uploading the PDB file of ligand

**URL:** <https://ask.bioexcel.eu/t/error-in-uploading-the-pdb-file-of-ligand/5304>\
**Category:** HADDOCK\
**Tags:** haddock\
**Created:** [October 22, 2024, 7:31am UTC](https://ask.bioexcel.eu/t/error-in-uploading-the-pdb-file-of-ligand/5304 "2024-10-22T07:31:14Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Yvette68](https://avatars.discourse-cdn.com/v4/letter/y/d2c977/32.png) [@Yvette68](https://ask.bioexcel.eu/u/Yvette68)\
**Post date:** [October 22, 2024, 7:31am UTC](https://ask.bioexcel.eu/t/error-in-uploading-the-pdb-file-of-ligand/5304/1 "2024-10-22T07:31:14Z")

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Hi,

I am getting the following error when uploading my ligand file:  
Error in PDB file. Unknown error: string index out of range  
Attached are several lines in my pdb file. Could you please tell me how to fix it? Thank you very much!

HETATM 1 C 1 4.551 14.837 2.758 0.00 0.00 C  
HETATM 2 C 1 5.605 13.836 3.219 0.00 0.00 C  
HETATM 3 C 1 4.946 12.629 3.878 0.00 0.00 C  
HETATM 4 C 1 3.849 12.060 2.987 0.00 0.00 C  
HETATM 5 C 1 3.477 14.146 1.929 0.00 0.00 C

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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 22, 2024, 8:02am UTC](https://ask.bioexcel.eu/t/error-in-uploading-the-pdb-file-of-ligand/5304/2 "2024-10-22T08:02:24Z")

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Several issues with that file:

1. It does not follow the correct PDB format

2. Each atom must have a unique atom name

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<div class="post-metadata">

**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [October 22, 2024, 8:05am UTC](https://ask.bioexcel.eu/t/error-in-uploading-the-pdb-file-of-ligand/5304/3 "2024-10-22T08:05:25Z")

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Dear Yvette68,

- Probably you want to check this resource to make sure your formatting follows the standards: [PDB format - Plouf](https://cupnet.net/pdb-format/)
- Each atom must have a unique name
- Checkout our tutorials at: [HADDOCK2.4 small molecule binding site screening – Bonvin Lab](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/) and [HADDOCK2.4 shape-restrained protein-small molecule tutorial – Bonvin Lab](https://www.bonvinlab.org/education/HADDOCK24/shape-small-molecule/)

Cheers

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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 22, 2024, 8:37am UTC](https://ask.bioexcel.eu/t/error-in-uploading-the-pdb-file-of-ligand/5304/4 "2024-10-22T08:37:10Z")

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Correction: for ligands it should remain HETATM

But the formatting of the file is important. It is not a space-separated format!

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**Author:** ![Yvette68](https://avatars.discourse-cdn.com/v4/letter/y/d2c977/32.png) [@Yvette68](https://ask.bioexcel.eu/u/Yvette68)\
**Post date:** [October 22, 2024, 12:37pm UTC](https://ask.bioexcel.eu/t/error-in-uploading-the-pdb-file-of-ligand/5304/5 "2024-10-22T12:37:21Z")

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Problem solved, thank you!

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**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [October 22, 2024, 12:50pm UTC](https://ask.bioexcel.eu/t/error-in-uploading-the-pdb-file-of-ligand/5304/6 "2024-10-22T12:50:14Z")

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Great to know !