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AMBER

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DESCRIPTION

Amber website  


Amber is a suite of biomolecular simulation programs. The term "Amber" refers to
two things. First, it is a set of molecular mechanical force fields for the
simulation of biomolecules; these force fields are in the public domain, and are
used in a variety of simulation programs. Second, it is a package of molecular
simulation programs which includes source code and demos.

Amber is distributed in two parts: AmberTools24 and Amber24. See the Download
Amber link for information on how to download the code.

Amber is developed in an active collaboration of David Case at Rutgers
University, Tom Cheatham at the University of Utah, Ray Luo at UC Irvine, Ken
Merz at Michigan State University, Maria Nagan at Stony Brook, Dan Roe at NIH,
Adrian Roitberg at the University of Florida, Carlos Simmerling at Stony Brook,
Junmei Wang at the University of Pittsburgh, Darrin York at Rutgers University,
and many others. Amber was originally developed under the leadership of Peter
Kollman.

A good general overview of the Amber codes can be found in:

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

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).

D.A. Case, H.M. Aktulga, K. Belfon, D.S. Cerutti, G.A. Cisneros, V.W.D.
Cruzeiro, 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).

See https://ambermd.org/AmberModels.php for information about force fields.


REQUIRED MODULES

For more details on specific modules required for different versions of AMBER,
run module spider amber. We currently support amber/24 (with cuda/12.4.1
openmpi/4.1.6 and gcc/12.2.0). Note that the Amber/24 (and Amber in general) is
provided to HiPerGator users by the courtesy of Prof. Adrian Roitberg. Amber
users are encouraged to register with Amber by downloading FREE version from
https://ambermd.org/GetAmber.php. Amber developers appreciate the courtesy.


SYSTEM VARIABLES

 * HPC_AMBER_DIR - installation directory
 * HPC_AMBER_BIN - executable program directory
 * HPC_AMBER_LIB - library directory
 * HPC_AMBER_INC - include file directory











CITATION

See https://ambermd.org/CiteAmber.php for how to cite Amber.




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