Amber Home Page   image of a piece of amber "insert clever motto here"
(Learn more about real Amber)

News

AmberTools15 was released on May 4, 2015


GTX-Titan-X Launched
AMBER 14 breaks MD speed record for a single desktop.


New 8 GPU Amber Certified GPU nodes now available with GTX-Titan-Black, K20 and K40 GPUs


Intel Xeon Phi support officially launched with latest update to PMEMD (AMBER 14)


Preinstalled Amber Certified GPU Workstations and Clusters now available with GTX-980, GTX-Titan-Black, K20, K40 and K80


Quick links

Amber force fields


Amber-related links
Benchmarks
GPU Support
Certified Hardware
File formats

Ordering Amber14
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: AmberTools15 and Amber14. You can use AmberTools15 without Amber14, but not vice versa. See below for information on how to obtain Amber14.

When citing Amber14 or AmberTools15 please use the following:

D.A. Case, J.T. Berryman, R.M. Betz, 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, T. Luchko, R. Luo, B. Madej, K.M. Merz, G. Monard, P. Needham, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, R. Salomon-Ferrer, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, D.M. York and P.A. Kollman (2015), AMBER 2015, University of California, San Francisco.

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 D.A. Case. Twenty-five years of nucleic acid simulations. Biopolymers, 99, 969-977 (2013).

For information about the GPU-accelerated code:

PME: R. Salomon-Ferrer, A.W. Goetz, D. Poole; S. Le Grand, and R.C. Walker Routine microsecond molecular dynamics simulations with AMBER - Part II: Particle Mesh Ewald. J. Chem. Theory Comput. 9, 3878-3888 (2013).

GB: A.W. Goetz, M.J. Williamson, D. Xu, D. Poole, S. Le Grand, and R.C. Walker. Routine microsecond molecular dynamics simulations with AMBER - Part I: Generalized Born. J. Chem. Theory Comput. 8, 1542-1555 (2012).
 

Some history:

2002 - 2008
     
2010 - 2013
     

AmberTools15 is now available!

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, with either explicit water or generalized Born solvent models. The sander program is now a part of AmberTools.

AmberTools15 (released on May 4, 2015) 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
sander Workhorse program for molecular dynamics simulations
mdgx Explicit solvent molecular dynamics simulations
ptraj and cpptraj Structure and dynamics analysis of trajectories
MMPBSA.py and amberlite Energy-based analyses of MD trajectories

Among the new features:
  • New generalized Born solvation parameters for nucleic acids
  • New ("OPC") explicit water model
  • New parameters for monatomic ions
  • Generation of an API for sander and mdgx, allowing their functionality to be accessed by third-party programs
  • Support for implicit membrane models in PB and FEW (free energy workflow)
  • Improved workflow for system preparation and validation
  • Major updates and extensions to the cpptraj program for trajectory analysis
    • energy: Simple energy calculation (faster than imin=5, no PME); calculate only terms you want.
    • areapermol: Simple area per molecule calculation (codifies what is done in lipid tutorial A16).
    • checkchirality: Action for checking amino acid chirality.
    • multivector: Action for calculating multiple vectors (e.g. all N-H vectors).
    • Some math operations can be performed on/between data sets (e.g. D0 = D1 + 2.3 etc).
    • Non-linear curve fitting
    • minimage: distance to next closest unit cell (atoms or center of mass), along with atom IDs. distance).
    • Imaging in 'hbond' command (distances and angles).
    • Non-orthogonal grids, normalize grids by density.
    • Vast improvements to 'nativecontacts' command, including time series generation.
    • Clustering: K-means, symmetric RMSD metric, pseudo-F and silhouette clustering metrics

  • More detailed changelog


Amber14 is now available!

We are pleased to announce the release (on April 15, 2014) of version 14 of the Amber software suite. (How to order.) This represents a significant update from version 12, which was released in April, 2012. (There was no "unlucky" Amber13.)

The Amber14 package builds on AmberTools15 by adding the pmemd program, which resembles the sander (molecular dynamics) code in AmberTools, but provides (much) better performance on multiple CPUs, and dramatic speed improvements on GPUs. In this release, more features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs.

General information

Code overview

The release consists of about 50 programs, that work reasonably well together. The major programs are as follows:
  • sander: Simulated annealing with NMR-derived energy restraints. This allows for NMR refinement based on NOE-derived distance restraints, torsion angle restraints, and penalty functions based on chemical shifts and NOESY volumes. Sander is also the "main" program used for molecular dynamics simulations, and is also used for replica-exchange, thermodynamic integration, and potential of mean force (PMF) calculations. Sander also includes QM/MM capability.
     
  • pmemd: This is an extensively-modified version (originally by Bob Duke) of the sander program, optimized for periodic, PME simulations, and for GB simulations. It is faster than sander and scales better on parallel machines. and it includes NVIDIA GPU acceleration. In the code model we are now following, sander is the vehicle to explore new features, and pmemd is a "production" code that implements sander's most-used features in a well-tested fashion that performs well in high-performance environments.
     
  • NAB: Originally named as "nucleic acid builder", NAB is a specialized language for writing programs that manipulate molecules and carry out molecular mechanics or distance-geometry based modeling. NAB provides and interface to Poisson-Boltzmann and RISM integral-equation solvent models. The "amberlite" package uses NAB to study protein-ligand interaction energetics.
  • LEaP: LEaP is an X-windows-based program that provides for basic model building and Amber coordinate and parameter/topology input file creation. It includes a molecular editor which allows for building residues and manipulating molecules.
     
  • antechamber: This program suite automates the process of developing force field descriptors for most organic molecules. It starts with structures (usually in PDB format), and generates files that can be read into LEaP for use in molecular modeling. The force field description that is generated is designed to be compatible with the usual Amber force fields for proteins and nucleic acids. The MCPB code can assist in generating force fields for metal centers.
     
  • ptraj and cpptraj: These are used to analyze MD trajectories, computing a variety of things, like RMS deviation from a reference structure, hydrogen bonding analysis, time-correlation functions, diffusional behavior, and so on.
     
  • mm_pbsa and mmpbsa.py: These are scripts that automate post-processing of MD trajectories, to analyze energetics using continuum solvent ideas. It can be used to break energies energies into "pieces" arising from different residues, and to estimate free energy differences between conformational basins.

Benchmarks

Downloads

Amber-related links

Amber-containing medicine from Poland

The force field

Note: All Amber force field parameter files can be obtained by downloading AmberTools15, and extacting the tar file. Parameter files will be in the amber14/dat/leap directory tree.

How to obtain the Amber14 program package

General correspondence

The AMBER Mail Reflector


Amber The Mail Reflector exists to provide a forum for discussions on the use of the Amber software and for release of bugfixes. Before posting please read the manual, consult the FAQ, and search the previous items discussed on the Amber Reflector using the Google search box provided on the archive site.
Mail reflectors distribute mail sent to the reflector address to all subscribers.

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.

Amber developers

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:
front row:Jim Caldwell, Kennie Merz, Carlos Simmerling, Ray Luo
back row:Dave Case, Piotr Cieplak, Mike Crowley, Tom Cheatham, Tom Darden, Junmei Wang.

And, below, a older photo of Peter and Tom Cheatham.


St. Simon Island, 2007


St. Simon Island, 2009


Stony Brook, 2010


Athens, Georgia, 2011


Rutgers, 2012


Salt Lake City, 2013


Stony Brook, 2014


Gainesville, 2015

The Amber15 authors are: D.A. Case, J.T. Berryman, R.M. Betz, 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, T. Luchko, R. Luo, B. Madej, K.M. Merz, G. Monard, P. Needham, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, R. Salomon-Ferrer, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, D.M. York 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


Last modified: .