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
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?
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.