Inclusion of N-methylated residues in peptides

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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

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.

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?

For example, I want to methylate the aromatic nitrogen of the Trp residue.

Ah - now I understand - unfortunately this is not supported.

The list of supported modified amino acids can be found at:

Thank you

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?

Not supported unfortunately