Assisted Model Building with Energy Refinement (AMBER)
Original author(s)Peter Kollman, David Case, Tom Cheatham, Ken Merz, Adrian Roitberg, Carlos Simmerling, Ray Luo, Junmei Wang, Ross Walker
Developer(s)University of California, San Francisco
Initial release2002; 20 years ago (2002)
Stable release
Amber20, AmberTools20[1] / April 31, 2020; 2 years ago (2020-04-31)
Written inC, C++, Fortran
Operating systemWindows, OS X, Linux, Unix, CNK
Platformx86, Nvidia GPUs, Blue Gene
SizeVaries
Available inEnglish
TypeMolecular dynamics
LicenseAmber: Proprietary
AmberTools: GPL, public domain, other open-source
Websiteambermd.org
AMBER is used to minimize the bond stretching energy of this ethane molecule.
AMBER is used to minimize the bond stretching energy of this ethane molecule.

Assisted Model Building with Energy Refinement (AMBER) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields. It is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Adrian Roitberg at University of Florida, Ken Merz at Michigan State University, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals.

Force field

The term AMBER force field generally refers to the functional form used by the family of AMBER force fields. This form includes several parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name.

Functional form

The functional form of the AMBER force field is[2]

Despite the term force field, this equation defines the potential energy of the system; the force is the derivative of this potential relative to position.

The meanings of right hand side terms are:

The form of the van der Waals energy is calculated using the equilibrium distance () and well depth (). The factor of ensures that the equilibrium distance is . The energy is sometimes reformulated in terms of , where , as used e.g. in the implementation of the softcore potentials.

The form of the electrostatic energy used here assumes that the charges due to the protons and electrons in an atom can be represented by a single point charge (or in the case of parameter sets that employ lone pairs, a small number of point charges.)

Parameter sets

To use the AMBER force field, it is necessary to have values for the parameters of the force field (e.g. force constants, equilibrium bond lengths and angles, charges). A fairly large number of these parameter sets exist, and are described in detail in the AMBER software user manual. Each parameter set has a name, and provides parameters for certain types of molecules.

Software

The AMBER software suite provides a set of programs to apply the AMBER forcefields to simulations of biomolecules. It is written in the programming languages Fortran 90 and C, with support for most major Unix-like operating systems and compilers. Development is conducted by a loose association of mostly academic labs. New versions are released usually in the spring of even numbered years; AMBER 10 was released in April 2008. The software is available under a site license agreement, which includes full source, currently priced at US$500 for non-commercial and US$20,000 for commercial organizations.

Programs

See also

References

  1. ^ Amber 2020 Reference Manual
  2. ^ Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995). "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules". J. Am. Chem. Soc. 117 (19): 5179–5197. CiteSeerX 10.1.1.323.4450. doi:10.1021/ja00124a002.
  3. ^ Maier, James A; Martinez, Carmenza; Kasavajhala, Koushik; Wickstrom, Lauren; Hauser, Kevin E; Simmerling, Carlos (2015). "Ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB". Journal of Chemical Theory and Computation. 11 (8): 3696–3713. doi:10.1021/acs.jctc.5b00255. PMC 4821407. PMID 26574453.
  4. ^ "The Amber Force Fields".
  5. ^ Dickson, Callum J; Madej, Benjamin D; Skjevik, Åge A; Betz, Robin M; Teigen, Knut; Gould, Ian R; Walker, Ross C (2014). "Lipid14: The Amber Lipid Force Field". Journal of Chemical Theory and Computation. 10 (2): 865–879. doi:10.1021/ct4010307. PMC 3985482. PMID 24803855.

Related reading

1. Duan, Yong; Wu, Chun; Chowdhury, Shibasish; Lee, Mathew C.; Xiong, Guoming; Zhang, Wei; Yang, Rong; Cieplak, Piotr; et al. (2003). "A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations". Journal of Computational Chemistry. 24 (16): 1999–2012. doi:10.1002/jcc.10349. PMID 14531054. S2CID 283317.