AMBER formula

Following on from our previous bucket list release on the CHARMM MD package and force fields, we now choose to introduce Amber, another MD simulation package and force field family that are frequently employed for biomolecular simulations in drug discovery. Like CHARMM, the Amber MD software originated in the late 1970s and has been maintained and expanded throughout the years. Following over a decade of model refinement and optimisation, the modern family of Amber force fields began with the development of the Cornell et al. force field in 1995 (commonly referred to as ff94), with the potential energy equation including bonded and non-bonded terms and parameters for amino acids and nucleic acids. Importantly, Cornell et al. established a general parameterisation procedure to ensure continuity and additivity for future iterations of molecule parameterisation. The procedure involves the derivation of partial atomic charges from an electrostatic potential, determined using QM calculations with the 6-31G* basis set, followed by two-stage restrained electrostatic potential (RESP) fitting. Since ff94, many refinements, corrections and additions to the Amber force field have been published, including ff14SB and LIPID14, that include parameters for amino acids, nucleic acids, carbohydrates and lipids. There is also a general amber force field (GAFF) that, like CGenFF, allows anyone to parameterise small molecules in a consistent way to the biomolecular force fields, allowing the interactions between drug molecules and their targets to be explored using simulation.

The Amber biomolecular simulation programs.

J Comp Chem. 2005. 26(16) 1668-1688

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules.

JACS. 1995. 117(19). 5179-5197.

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

J. Chem. Theory Comput. 2015. 11(8). 3696-3713.

Lipid14: The Amber Lipid Force Field.

J. Chem. Theory Comput. 2014. 10(2). 865-879. 

Development and testing of a general amber force field.

J. Comput. Chem. 2004. 25(9). 1157-1174.

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