# Inclusion of N-methylated residues in peptides **URL:** \ **Category:** HADDOCK\ **Created:** [September 20, 2023, 5:57am UTC](https://ask.bioexcel.eu/t/inclusion-of-n-methylated-residues-in-peptides/4540 "2023-09-20T05:57:58Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![John](https://avatars.discourse-cdn.com/v4/letter/j/a3d4f5/32.png) [@John](https://ask.bioexcel.eu/u/John)\ **Post date:** [September 20, 2023, 5:57am UTC](https://ask.bioexcel.eu/t/inclusion-of-n-methylated-residues-in-peptides/4540/1 "2023-09-20T05:57:59Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [HADDOCK – Bonvin Lab](http://www.bonvinlab.org/software/haddock2.4) I wanted to include N-methylated residues in my peptide for docking. What is the way to incorporate such residues in the pdb file. For reference, I need N-methyl Trp, Ile and Gly I tried directly adding the residues using pymol and renaming the pdb file. But haddock didn’t recognize those residues while docking. Any input or suggestions will be greatly appreciated JR ---
**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 20, 2023, 6:12am UTC](https://ask.bioexcel.eu/t/inclusion-of-n-methylated-residues-in-peptides/4540/2 "2023-09-20T06:12:40Z")
You will have to add one additional residue on the Nter (e.g. a GLY) and rename the residue to NME for HADDOCK to recognise it. Don’t worry about adding/deleting atoms, HADDOCK will handle that. ---
**Author:** ![John](https://avatars.discourse-cdn.com/v4/letter/j/a3d4f5/32.png) [@John](https://ask.bioexcel.eu/u/John)\ **Post date:** [September 20, 2023, 6:20am UTC](https://ask.bioexcel.eu/t/inclusion-of-n-methylated-residues-in-peptides/4540/3 "2023-09-20T06:20:45Z")
My residues are not all in the terminus… So should my pdb file contain Gly normal cordinates and another Nme corodinate… Can you please elaborate? ---
**Author:** ![John](https://avatars.discourse-cdn.com/v4/letter/j/a3d4f5/32.png) [@John](https://ask.bioexcel.eu/u/John)\ **Post date:** [September 20, 2023, 6:21am UTC](https://ask.bioexcel.eu/t/inclusion-of-n-methylated-residues-in-peptides/4540/4 "2023-09-20T06:21:41Z")
For example, I want to methylate the aromatic nitrogen of the Trp residue. ---
**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 20, 2023, 6:33am UTC](https://ask.bioexcel.eu/t/inclusion-of-n-methylated-residues-in-peptides/4540/5 "2023-09-20T06:33:34Z")
Ah - now I understand - unfortunately this is not supported. The list of supported modified amino acids can be found at: [https://bianca.science.uu.nl/haddock2.4/library](https://bianca.science.uu.nl/haddock2.4/library) ---
**Author:** ![John](https://avatars.discourse-cdn.com/v4/letter/j/a3d4f5/32.png) [@John](https://ask.bioexcel.eu/u/John)\ **Post date:** [September 20, 2023, 7:47am UTC](https://ask.bioexcel.eu/t/inclusion-of-n-methylated-residues-in-peptides/4540/6 "2023-09-20T07:47:37Z")
ohh…ok Thank you ---
**Author:** ![John](https://avatars.discourse-cdn.com/v4/letter/j/a3d4f5/32.png) [@John](https://ask.bioexcel.eu/u/John)\ **Post date:** [September 22, 2023, 10:38am UTC](https://ask.bioexcel.eu/t/inclusion-of-n-methylated-residues-in-peptides/4540/7 "2023-09-22T10:38:20Z")
Can I methylate an internal amide in a peptide For example in peptide GCYKL, I need N-methylated tyrosine (GCY(Nme)KL. Can this be done somehow? ---
**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 22, 2023, 11:13am UTC](https://ask.bioexcel.eu/t/inclusion-of-n-methylated-residues-in-peptides/4540/8 "2023-09-22T11:13:38Z")
Not supported unfortunately