How to cite Amber
When citing Amber22 or AmberTools22 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, R.E.
Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S.
Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T.
Kurtzman, T.S. Lee, S. LeGrand, 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, R.M. Wolf, X.
Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022, 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)
|
