AMBER is a suite of programs for use in molecular modeling and molecular simulations. It consists of a substructure database, a force field parameter file, and a variety of useful programs. Here we give some commented sample runs to provide an overview of how things are carried out. The examples do not use the interface programs, and only a cover a fraction of the things that it is possible to do with AMBER. The formats of the example files shown are described in detail later in the manual, in the chapters pertaining to the programs.
The files used in these examples are in the $AMBERHOME/examples
subdirectory.
Additional tutorial examples are available on at
http://www.amber.ucsf.edu/amber/.
You should also look at the sample inputs in the chapters devoted to each
program, especially for LEaP and sander.