Amber 2017 Reference Manual

(Covers Amber16 and AmberTools17)

Dear all,

Molecular dynamics simulations of proteins, which began about 25 years ago, are by now widely used as tools to investigate structure and dynamics under a variety of conditions. Molecular dynamics allows the study of biological and chemical systems at the atomistic level on timescales from femtoseconds to milliseconds. This technique complements experiments while offering a way to follow dynamic processes difficult to discern with experimental techniques.

“Amber” is the collective name for a suite of molecular simulation programs that allows users to carry out and analyze molecular dynamics simulations, particularly for proteins, nucleic acids and carbohydrates. Amber package allows to study a wide variety of molecular biology problems, such as ligand binding, enzyme reaction, protein-protein interactions, protein folding, refinement of structures and much more.

The BKU Unit has recently purchased the most up to date version of Amber (v. 16). This version represents a significant improvement, providing new methodological improvements, such as simulation of crystal lattices, and specially allows a dramatic improvement in computational speed. This in turns allows to study much larger systems during much longer simulation time, providing more accurate energetic estimations and more realistic simulations.

If you are interested in knowing more about Amber and structural dynamics simulations, please contact us for an initial discussion.

Best wishes,

Fabian