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AmberTools13 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

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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:
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. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, 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 (2012), AMBER 12, University of California, San Francisco.

For use of the GPU accelerated code please also cite the following:
Andreas W. Goetz; Mark J. Williamson; Dong Xu; Duncan Poole; Scott Le Grand; & Ross C. Walker* "Routine microsecond molecular dynamics simulations with AMBER - Part I: Generalized Born", J. Chem. Theory Comput., (2012), 8 (5), pp 1542-1555 , DOI: 10.1021/ct200909j
 

Amber developers, January 2012

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AmberTools13 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 (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

Amber12 is now available!

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:

  • Force fields: Amber has a new fixed-charge protein force field, ff12SB, enchanced support for polarizable potentials and a new modular lipid force field Lipid11 designed to be compatible with the other pairwise additive AMBER force fields.

  • Expanded options for numerical Poisson-Boltzmann solvation calculations, including models for membrane systems and support for periodic systems.

  • An enchanced 3D-RISM integral equation model, using the Kovalenko-Hirata (and other) closure approximations, with a better treatement of aqueous electrolytes.

  • Improved ideas for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.

  • Simplified installation and automatic update support.

  • Semi-empirical quantum calculations can use d-orbitals, allowing the use of Hamiltonian models such as AM1/d and PM6.

  • QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available.

  • More features from sander have been added to the pmemd code for both CPU and GPU, including Temperature Replica Exchange, Isotropic Periodic Sum, Accelerated Molecular Dynamics and support for various harmonic restraints based on the use of NMRopt on GPUs. Support is also included for the latest Kepler I (K10), Kepler II (K20) and GTX6XX GPUs.

  • Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations.

  • New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

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. Additionally, starting with version 11, 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

The force field

How to obtain the Amber12 program package

General correspondence

The AMBER Mail Reflector

 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, followed by a photo of the participants at the February, 2007 Amber Developers' Meetings on St. Simon Island, Georgia; more recent photos then follow.

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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