# Heme docking/ data preparation for HADDOCK

**URL:** <https://ask.bioexcel.eu/t/heme-docking-data-preparation-for-haddock/1739>\
**Category:** HADDOCK\
**Created:** [October 25, 2019, 9:11am UTC](https://ask.bioexcel.eu/t/heme-docking-data-preparation-for-haddock/1739 "2019-10-25T09:11:11Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![schachingerf](https://avatars.discourse-cdn.com/v4/letter/s/9de053/32.png) [@schachingerf](https://ask.bioexcel.eu/u/schachingerf)\
**Post date:** [October 25, 2019, 9:11am UTC](https://ask.bioexcel.eu/t/heme-docking-data-preparation-for-haddock/1739/1 "2019-10-25T09:11:11Z")

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Hi all,  
I just started to work with HADDOCK and have a general question. I want to dock a protein with a heme b to another protein. For that as far as I understood I need to rename the residue HEM to HEB in the PyMol/ .pdb file and in the topology file I need to name the HEB and FE from HETATM to ATOM so that HADDOCK can proccess the data.  
I am not sure how to do this and would be thankful if you can help me please.

- can I use the alter command, if yes, how?
- or ii also tried to open the file in editor, do the changes but then I have a .txt file that i cannot use anymore as I need a .pdb file for HADDOCK.  
Thank you for helping me!

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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 25, 2019, 9:35am UTC](https://ask.bioexcel.eu/t/heme-docking-data-preparation-for-haddock/1739/2 "2019-10-25T09:35:15Z")

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Check: [https://milou.science.uu.nl/services/HADDOCK2.2/library.html](https://milou.science.uu.nl/services/HADDOCK2.2/library.html)

The bottom of that page provide links to example PDB files.

When editing your files, make sure to use a simplex ASCII text editor and save the file as ASCII text with .pdb as extension.