How to cite Amber
When citing Amber24 or AmberTools25 please use the following:
1) D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R.
Brozell, F.S. Carvahol, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro,
T.A. Darden, N. Forouzesh, M. Ghazimirsaeed, G. Giambaşu, T. Giese, M.K.
Gilson, H. Gohlke, A.W. Goetz, J. Harris, Z. Huang, S. Izadi, S.A. Izmailov,
K. Kasavajhala, M.C. Kaymak, I. Kolossv\'a ry, A. Kovalenko, T. Kurtzman,
T.S. Lee, P. Li, Z. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, M.
Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A.
O'Hearn, A. Onufriev, F. Pan, S. Pantano, 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, X. Wu, Y. Wu, Y. Xiong, Y. Xue, D.M. York, C. Zhao, Q. Zhu, and P.A. Kollman (2025), Amber 2025, University of California, San Francisco.
2) D.A. Case, H.M. Aktulga, K. Belfon, D.S. Cerutti, G.A. Cisneros, V.W.D. Cruz
eiro, N. Forouzesh, T.J. Giese, A.W. Götz, H. Gohlke, S. Izadi, K. Kasavajhala,
M.C. Kaymak, E. King, T. Kurtzman, T.-S. Lee, P. Li, J. Liu, T. Luchko, R. Luo,
M. Manathunga, M.R. Machado, H.M. Nguyen, K.A. O’Hearn, A.V. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T.E. Cheatham III, D.R. Roe, A. Roitberg, C. Simmerling, D.M. York, M.C. Nagan, and K.M. Merz Jr. AmberTools.
J. Chem. Inf. Model. 63, 6183-6191 (2023).
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)
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