I have a peptide with N and C terminus modified with Acetyl group at the N-terminus and NH2 at the Cterminus. I put in the sequence the ACE residue and CTN but it gives me an error saying it doesnt recognize the topology of these residues. I used also the B1N residue of the carbohydrates topology file for the Nacetylglusomine but it doesn’t recognize either this residue. How can i do to set up these residues in my protein?
Did you check that you’re using the right atoms for these two residues? You can find the list of the proper atoms for residues ACE and CTN there: http://milou.science.uu.nl/services/HADDOCK2.2/library.html
B1N is not part of modified amino-acids supported by HADDOCK so you’ll need to define it as HETATM in your PDB file and get its topology be defined by PRODRG during the HADDOCK run.
Edit: To be complete, ACE and CTN are two groups you’ll add complementary to the residues they are attached to, do not replace the whole residue with them.
I hope this will help,