AMBER 7 is a package of molecular simulation programs useful for performing calculations on proteins and DNA.
Academic users can purchase a license for around $US 400.
Much useful information can be found at http://amber.scripps.edu
In particular, the users manual can be found at http://amber.scripps.edu/doc7/amber7.pdf
Other important tips are to have the AMBERHOME environment variable set e.g. in the bash
>export AMBERHOME=/usr/local/amber7 # or wherever it happens to be.
and to add the exe directory to your path. Again in the bash:
Note, you can also find the users manual at $AMBERHOME/doc/amber7.pdf