# Preparing small molecules for docking

**URL:** <https://ask.bioexcel.eu/t/preparing-small-molecules-for-docking/4451>\
**Category:** HADDOCK\
**Created:** [August 17, 2023, 4:01pm UTC](https://ask.bioexcel.eu/t/preparing-small-molecules-for-docking/4451 "2023-08-17T16:01:04Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![JHlatt](https://avatars.discourse-cdn.com/v4/letter/j/5f9b8f/32.png) [@JHlatt](https://ask.bioexcel.eu/u/JHlatt)\
**Post date:** [August 17, 2023, 4:01pm UTC](https://ask.bioexcel.eu/t/preparing-small-molecules-for-docking/4451/1 "2023-08-17T16:01:04Z")

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I am trying to dock small molecules with my protein. Sorry this might seem a basic question but I am struggling to prepare the pdb file for the small molecule.

I have a small molecule in pdb format. When uploaded to the web server I receive this error message “Your PDB contains multiple residues with number 0 in chain or duplicated atom names.”

Sorry I can’t find anything in a tutorial and I’m not sure what changes need to be made to the pdb text file to fix this. If you have any advice that would be great.

Thank you

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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:** [August 17, 2023, 5:57pm UTC](https://ask.bioexcel.eu/t/preparing-small-molecules-for-docking/4451/2 "2023-08-17T17:57:33Z")

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All atom names must be unique

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<div class="post-metadata">

**Author:** ![JHlatt](https://avatars.discourse-cdn.com/v4/letter/j/5f9b8f/32.png) [@JHlatt](https://ask.bioexcel.eu/u/JHlatt)\
**Post date:** [August 18, 2023, 9:19am UTC](https://ask.bioexcel.eu/t/preparing-small-molecules-for-docking/4451/3 "2023-08-18T09:19:23Z")

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Thank you, I renumbered the atoms in the text file and now it works. The next problem however is the on the in put parameters page. I need to pick active residues. The only residue available for the ligand is ‘x’ and the webserver won’t allow this as a selection. How do I get passed this? (I have uploaded an image to help explain what I mean.

 ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/51c0446ee1d0e1976d74d9bcf77f205d832da9de.png)

Thank you

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<div class="post-metadata">

**Author:** ![JHlatt](https://avatars.discourse-cdn.com/v4/letter/j/5f9b8f/32.png) [@JHlatt](https://ask.bioexcel.eu/u/JHlatt)\
**Post date:** [August 18, 2023, 9:28am UTC](https://ask.bioexcel.eu/t/preparing-small-molecules-for-docking/4451/4 "2023-08-18T09:28:56Z")

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Sorry please ignore that last question. I realised I was typing ‘x’ rather than ‘0’!!!

However, I am having a problem selecting the ‘x’ residue for my protein which is an iron. important for ligand binding. The error says ‘none of the active residues are accessible’ when I try to select the iron. I know it is accessible as things bind to it, is there anything I can do to help the programme recognise this?

Thank you

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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:** [August 18, 2023, 6:40pm UTC](https://ask.bioexcel.eu/t/preparing-small-molecules-for-docking/4451/5 "2023-08-18T18:40:32Z")

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If you ask for elevated access level in your registration page you can turn off the option to filter out buried residues.