Amber masthead
Filler image AmberTools23 Amber22 Manuals Tutorials Force Fields Contacts History
Filler image

Useful links:

Amber Home
Download Amber
Amber Citations
GPU Support
Mailing Lists
For Educators
File Formats

How to cite Amber

When citing Amber22 or AmberTools23 please use the following:
D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, N. Forouzesh, G. Giambaşu, T. Giese, M.K. Gilson, H. Gohlke, A.W. Goetz, J. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, H. Wei, X. Wu, Y. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, Q. Zhu, and P.A. Kollman (2023), Amber 2023, University of California, San Francisco.

Also, please visit the contributors page for more complete information about who has done what over the years.

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 and ff19SB protein force fields are here:
C.Tian, K. Kasavajhala, K. A. A. Belfon, L. Raguette, H. Huang, A. N. Migues J. Bickel, Y. Wang, J. Pincay, Q. Wu and C. Simmerling. (2019) "ff19SB: Amino-Acid-Specific Protein Backbone Paramters Trained against Quantum Mechanics Energy Surfaces in Solution." J. Chem. Theory Comput.16, 528-552. (link)

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)

"How's that for maxed out?"

Last modified: Sep 18, 2023