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How to cite Amber

When citing Amber16 or AmberTools17 please use the following:
D.A. Case, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, D. Greene, N. Homeyer, S. Izadi, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D. Mermelstein, K.M. Merz, G. Monard, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, C.L. Simmerling, W.M. Botello-Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2017), AMBER 2017, University of California, San Francisco.

A good general overview of the Amber codes can be found in:
R. Salomon-Ferrer, D.A. Case, R.C. Walker. (2013) "An overview of the Amber biomolecular simulation package." WIREs Comput. Mol. Sci. 3, 198-210. (PDF)
D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. (2005) "The Amber biomolecular simulation programs." J. Computat. Chem. 26, 1668-1688. (link)

An overview of the Amber protein force fields, and how they were developed, can be found in:
J.W. Ponder and D.A. Case. (2003) "Force fields for protein simulations." Adv. Prot. Chem. 66, 27-85. (PDF)

Details on the ff14SB force field are here:
J.A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K.E. Hauser and C. Simmerling. (2015) "ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB." J. Chem. Theory Comput. 11, 3696-3713. (link)

Similar information for nucleic acids is given by:
T.E. Cheatham, III and D.A. Case. (2013) "Twenty-five years of nucleic acid simulations." Biopolymers, 99, 969-977. (link)

For information on the GPU-accelerated code, please see:
A.W. Goetz, M.J. Williamson, D. Xu, D. Poole, S. Le Grand, and R.C. Walker. (2012) "Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born." J. Chem. Theory Comput. 8, 1542-1555. (link)
R. Salomon-Ferrer, A.W. Goetz, D. Poole; S. Le Grand, and R.C. Walker. (2013) "Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent Particle Mesh Ewald." J. Chem. Theory Comput. 9, 3878-3888. (link)

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Last modified: Feb 10, 2018