Problems in running HADDOCK with an amidated peptide at c-terminus

HADDOCK
1

I’m trying to do a job in HADDOCK with an amidated peptide in the c-terminus. However, I can’t because the following message always appears: "The following error occurred when processing one of your PDB file: Unable to generate topology for ligand NHH. PRODGR did not create the required output. PRODGR> WARNING: deleted hydrogen H1 from your input.PRODGR> WARNING: deleted hydrogen H2 from your input.

What can i do in this situation?

Thanks

2

Add one additional residue to your PDB file and change its residue name to CTN

See HADDOCK Web Server - Settings

And simply defined as ATOM and not HETATM

3

Sorry, I did not understand how to do this. I’ve recently started using HADDOCK

4

Add one amino acid to your peptide (e.g. can be done in PyMol, adding one GLY residue), edit the PDB file with a text editor the file and change its name to CTN

5

OK. And after doing that, how do I set it as atom and not to HETATM ?

6

Edit the PDB file simply. It’s an ASCII text file.

When doing that make sure to keep the right column order