The release consists of about 60 programs, that work reasonably well together. Normal mode analysis program using first and second derivative information, used to find search for local minima, perform vibrational analysis, and search for transition states. It includes a molecular editor which allows for building residues and manipulating molecules. For example, one might define a torsional restraint whose target value changed on each iteration of a DO-loop. This makes it easy to perform torsional driving, for example.
Manuals are available in html and pdf formats.
Setting up Environment You may choose any of the following methods to access Amber. Control input files will be required for modules such as sander and the user is responsible for the generation of such files according to the user's specific needs. It is recommended to create a script similar to the one given below to submit you sander job to the LSF batch queue. The following LSF command at Chastity prompt wil submit the job to the LSF batch queue. The default Amber version is 6.