# Docking peptides with modified amino acids

**URL:** <https://ask.bioexcel.eu/t/docking-peptides-with-modified-amino-acids/1990>\
**Category:** HADDOCK\
**Created:** [May 5, 2020, 8:17am UTC](https://ask.bioexcel.eu/t/docking-peptides-with-modified-amino-acids/1990 "2020-05-05T08:17:40Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![shrutivijayk](https://avatars.discourse-cdn.com/v4/letter/s/65b543/32.png) [@shrutivijayk](https://ask.bioexcel.eu/u/shrutivijayk)\
**Post date:** [May 5, 2020, 8:17am UTC](https://ask.bioexcel.eu/t/docking-peptides-with-modified-amino-acids/1990/1 "2020-05-05T08:17:40Z")

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Hi,  
My peptide has several N-methylated amino acids and HADDOCK fails as it cannot recognize them. Not all of my residues are included here - [http://haddock.science.uu.nl/services/HADDOCK/library.html](http://haddock.science.uu.nl/services/HADDOCK/library.html)  
Is there still any way to use HADDOCK to still dock the peptide? Is it possible with the expert interface? How do I register for that?  
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:** [May 5, 2020, 9:32am UTC](https://ask.bioexcel.eu/t/docking-peptides-with-modified-amino-acids/1990/2 "2020-05-05T09:32:20Z")

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Unfortunately if the residues are not listed in the list of supported modified amino acids you won’t be able to use HADDOCK for this.  
Topologies and parameters would have to be defined for those (and you can’t upload those to the server).

As for expert access, you can request it in your registration page.

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**Author:** ![Omar](https://avatars.discourse-cdn.com/v4/letter/o/f0a364/32.png) [@Omar](https://ask.bioexcel.eu/u/Omar)\
**Post date:** [February 25, 2023, 2:48pm UTC](https://ask.bioexcel.eu/t/docking-peptides-with-modified-amino-acids/1990/3 "2023-02-25T14:48:41Z")

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Are we still unable to upload parameter files of modified residues (beta-Lysine in my case in a protein-nucleic acid docking) to the web portal ?  
also would like to know how these parameter files are made, any tutorials on them?

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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:** [February 25, 2023, 3:51pm UTC](https://ask.bioexcel.eu/t/docking-peptides-with-modified-amino-acids/1990/4 "2023-02-25T15:51:14Z")

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No support for modified parameter files and topologies.

You would have to run a local version for that.

And we don’t have any tutorial on how to generate custom topo/param files I am afraid. Not so trivial…