What is AMBER?
At its core, AMBER – the acronym for Assisted Model Building with Energy Refinement (AMBER) – is the “. . . collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules.” (AMBER 2018 Reference Manual.) It primarily focuses on enabling simulation of enzymes involved in biocatalysis and the interaction between drug candidates and protein receptors. It is a tool broadly used across the pharmaceutical industry to aid in target identification and validation, lead discovery and lead optimization. According to the NCBI National Center for Biotechnology Information (NCBI), “Modeling and simulation techniques have for some time been an important feature of biocatalysis research, often applied as a complement to experimental studies.”
Delving deeper, AMBER consists of both a set of molecular mechanical force fields for the simulation of biomolecules as well as the molecular simulation suite that implements these force fields.
AMBER was established through the foundational contributions of Professor Peter A. Kollman at the University of California, San Francisco in the 1970’s.
Fast forwarding to today, the current AMBER software suite is divided into two parts:
- AmberTools18, a collection of freely available programs for biomolecular simulation and analysis.
- Amber18, which is centered around the pmemd simulation program (“pmemd” stands for “Particle Mesh Ewald Molecular Dynamics”).