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NewsAmberTools13 released on April 22, 2013 Jan 2013, Kepler K20/K20X GPU Benchmarks and Updated Recommended GPU Hardware Nov 2012, AMBER MD Workstations Announced - Recommended Hardware for GPU Acceleration Sep 2012, Major GPU Update Patch Released Quick linksAmber-related links Benchmarks GPU Support File formats Ordering Amber12 Mailing lists |
Assisted Model Building with Energy Refinement
"Amber" refers to two things: a set of molecular mechanical
force fields for the simulation of biomolecules (which are
in the public domain, and are used
in a variety of simulation programs); and a package of
molecular
simulation programs which includes source code and demos.
Amber is distributed in two parts:
AmberTools13 and Amber12. You
can use AmberTools13 without Amber12, but not vice versa. See below for information on how to obtain Amber12.
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).
(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. The Amber biomolecular
simulation programs. J. Computat. Chem. 26, 1668-1688 (2005).
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 M.A. Young. Molecular
dynamics simulation of nucleic acids: Successes, limitations and promise.
Biopolymers 56, 232-256 (2001).
Please cite the use of AMBER 12 and AmberTools 13 as:
For use of the GPU accelerated code please also cite the following: ![]() Amber developers, January 2012
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AmberTools consists of several independently developed packages that work well
by themselves, and with Amber itself. The suite can also be used to carry
out complete molecular dynamics simulations (using NAB or mdgx), with either
explicit water or generalized Born solvent models.
AmberTools13 (released on April 22, 2013) consists of the following main codes:
| NAB | build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models |
| antechamber and MCPB | Create force fields for general organic molecules and metal centers |
| tleap | Basic preparation program for Amber simulations |
| sqm | semiempirical and DFTB quantum chemistry program |
| pbsa | Performs numerical solutions to Poisson-Boltzmann models |
| 3D-RISM | Solves integral equation models for solvation |
| mdgx | Code for explicit solvent molecular dynamics simulations |
| ptraj and cpptraj | Structure and dynamics analysis of trajectories |
| MMPBSA.py and amberlite | Energy-based analyses of MD trajectories |
We are happy to announce the release (on April 4, 2012) of version 12 of the Amber software suite. (How to order.) This represents a significant update from version 11, which was released in April, 2010. The major differences include:
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General information
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Code overview
The release consists of about 50 programs, that work reasonably well
together. The major programs are as follows:
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Only subscribers to the reflector can post.
To join/unjoin the reflector, please see:
http://lists.ambermd.org/mailman/listinfo/amber
To post or mail to the list (subscribers only), e-mail (in plain text) to:
Please use this list for discussion of Amber-specific issues only; in particular, announcements of general interest to the online chemistry community should be sent to the community's main reflector, chemistry@ccl.net. Amber users are encouraged to join this list as well, since it has a lot of useful information and since many other programs also use the Amber force fields.
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Amber is developed in an active collaboration of
David Case
at Rutgers University,
Tom Cheatham at
the University of Utah,
Ken Merz and
Adrian Roitberg at Florida,
Carlos Simmerling at
SUNY-Stony Brook,
Ray Luo at UC Irvine,
Junmei
Wang at UT Southwestern,
Ross Walker at UC San Diego, and
many others.
Amber was originally developed under the leadership of
Peter Kollman.
The photo at the left shows the Amber crew at its October, 2004 meeting in Stony Brook. Below that is a group photo a joint CHARMM/Amber developers' meeting held in San Diego in July, 2003. At the bottom left is an older
photo of Amber developers, from a meeting in San Francisco in November,
2001: And, below, a older photo of Peter and Tom Cheatham, followed by a photo of
the participants at the February, 2007 Amber Developers' Meetings on St. Simon
Island, Georgia; more recent photos then follow.
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St. Simon Island, 2009

Stony Brook, 2010

Athens, Georgia, 2011

Rutgers, 2012

Salt Lake City, 2013
The Amber 12 authors are: D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B.P. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Götz, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko and P.A. Kollman.
Many people not listed in the author list helped add features to various codes; these contributions are outlined here.
| Amber developers at work | Amber developers at play | Amber users after reading our documentation |
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