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?
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
Sorry, I did not understand how to do this. I’ve recently started using HADDOCK
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
OK. And after doing that, how do I set it as atom and not to HETATM ?
Edit the PDB file simply. It’s an ASCII text file.
When doing that make sure to keep the right column order