> Does anyone know if it is possible to incorporate acetylation (Ac-) at the N-terminus and amidation (-NH2) at the C-terminus when doing a docking run? In my starting PDB file, these atoms are listed as HETATM and when I run dock, the output files no longer have the HETATM atoms. I have a case where the presence of these termini caps make a difference in experimental binding and would like to take a look at it using RosettaDock.
I had the same question. Rosetta would give error saying unrecognized residue. I guess, there is no direct/simpler way to include these (based on my email conversation with the developers). Please let me know if you are able to make progress along these lines.