Preparatory programs.

LEaP

is the primary program to create a new system in Amber, or to modify old systems. It combines the functionality of prep, link, edit, and parm from earlier versions.

PROTONATE

This program will add hydrogens in appropriate locations to peptides and proteins that lack them. It can also check the suitability of protons that are already present, and convert from one naming system to another (e.g. from IUPAC-IUB recommendations to Brookhaven format.)