# Heme b pdb file for docking

**URL:** <https://ask.bioexcel.eu/t/heme-b-pdb-file-for-docking/5273>\
**Category:** Uncategorized\
**Created:** [September 27, 2024, 9:18am UTC](https://ask.bioexcel.eu/t/heme-b-pdb-file-for-docking/5273 "2024-09-27T09:18:09Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![martimfrazao](https://avatars.discourse-cdn.com/v4/letter/m/2bfe46/32.png) [@martimfrazao](https://ask.bioexcel.eu/u/martimfrazao)\
**Post date:** [September 27, 2024, 9:18am UTC](https://ask.bioexcel.eu/t/heme-b-pdb-file-for-docking/5273/1 "2024-09-27T09:18:09Z")

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Hello all

I’m currently doing my master thesis and I wanted to perform the docking of heme b to a protein in order to get an idea on the docking site, but I’ve been having problems trying to get a working pdb file for the heme. The examples given on [HADDOCK Web Server - Settings](https://wenmr.science.uu.nl/haddock2.4/library) don’t seem to be working anymore, and the pdbs I’ve been using don’t allow me to change the charge of the iron, coming out with a topological error whenever I do so. My question is if it’s not possible to change the charge of the heme iron, or if it requires something other than just changing the pdb.

Thank you in advance,  
Martim

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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:** [September 27, 2024, 10:43am UTC](https://ask.bioexcel.eu/t/heme-b-pdb-file-for-docking/5273/2 "2024-09-27T10:43:08Z")

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Check [https://rascar.science.uu.nl/haddock2.4/library](https://rascar.science.uu.nl/haddock2.4/library) for an example of how to define the metals in a PDB file

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**Author:** ![martimfrazao](https://avatars.discourse-cdn.com/v4/letter/m/2bfe46/32.png) [@martimfrazao](https://ask.bioexcel.eu/u/martimfrazao)\
**Post date:** [September 30, 2024, 9:34am UTC](https://ask.bioexcel.eu/t/heme-b-pdb-file-for-docking/5273/3 "2024-09-30T09:34:36Z")

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I have followed those examples, specifically this one for the heme iron.

 ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/2/29efd28d48d7208359186c24df70fb86409b86e0.png)

Can I change the charge of the iron on the pdb? Because the example given for ions is different.

> HETATM 3833 ZN+2 ZN2 A 42 21.391 -8.794 33.944 1.00 24.37 ZN

Thank you,  
Martim

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<div class="post-metadata">

**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:** [September 30, 2024, 9:52am UTC](https://ask.bioexcel.eu/t/heme-b-pdb-file-for-docking/5273/4 "2024-09-30T09:52:49Z")

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The iron in the heme is part of the heme and not a standard ion in that respect. You should not change it.

For other ions you can indeed specify the charge state.