It’s my first time trying to do docking and using Haddock, so I would like to ask any of you for some tips and pointers. I’m trying to simulate the covalent binding of a peptide with a modified side chain to a protein.
The modified side chain doesn’t exist in the PDB library, so I defined the whole residue with HETATM command, and used an CNS file to connect the N ter and Cter of the residue to the next and previous residue.
After docking I’ve noticed though that my modified residue had drifted away. How can I prevent that?
Also, I’m using Haddock, but without any experimental infos on the protein-peptide interaction apart from the bound lenght I want to create. So I was wondering if I want to perform ab initio calculations, which parameters should I choose?
Thank you very much in advance for your help!