Peptide with charged termini


I tried to dock a protein & a peptide with charged termini in the initial structure. It seems that during the preparation step the termini I’d like to keep are removed. Is this a problem of 1- topology, 2- option that are not accessible in the easy interface, 3- something else ?

Thanks for your help,


Hi Nicolas

Indeed the default is to have uncharged termini (since often what you are docking is not a full sequence).

You can however control that at the expert and higher interfaces by ticking the boxes under the molecule menu.

If you only have easy access, request higher level through the registration page.


Thanks a lot for the answer.