I am docking cyclic peptides to a protein, and I wondered wether the algorithm takes the charge of the atoms of the cyclic peptide into account or not. Should the cyclic peptide pdb be dominantly charged at pH7 or can it be neutral?
The force field we are using (and any force field in principle) assign partial charges to atoms.
Further there are the usual positively and negatively charged amino acids.
And histidine which can have various protonation states. The server will “guess” the most likely state using the reduce software.
Thank you very much for your quick response.
So did I understand correctly that for a neutral molecule (no charges on any amino acids), charges are assigned by haddock through the forcefield, the “usual” charge attribution and the “guess” function of the reduce software?