Software

The AMBER molecular modeling package


Amber developers, January, 2014

Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term amber is also sometimes used to refer to the empirical force field that is implemented here. It should be recognized however, that the code and force field are separate: several other computer packages have implemented the amber force field, and other force fields can be implemented with the amber programs. Further, the force field is in the public domain, whereas the codes are distributed under a license agreement.

A good general overview of the Amber codes can be found in: 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. The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668-1688 (2005).

R. Salomon-Ferrer, D.A. Case and R.C. Walker. An overview of the Amber biomolecular simulation package. WIREs: Comput. Mol. Sci., 3, 198-210 (2013).

An overview of the Amber protein force fields, and how they were developed, can be found in: J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85 (2003). Similar information for nucleic acids is given by T.E. Cheatham, III and D.A. Case, Twenty-five years of nucleic acid simulations. Biopolymers, 99, 969-977 (2013).

The most recent version of AMBER is version 16, released in April, 2016. It has a companion of AmberTools17, released in April 2017.

AMBER authors

D.A. Case, R.M. Betz, W. Botello-Smith, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, C. Lin, T. Luchko, R. Luo, B. Madej, D. Mermelstein, K.M. Merz, G. Monard, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, C. Sagui, C.L. Simmerling, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, L. Xiao, and P.A. Kollman.

The most complete and up-to-date information (including instructions on obtaining AMBER) is maintained here:

  • http://ambermd.org



    Updated on October 25, 2017. Comments to case@biomaps.rutgers.edu