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

News

NVIDIA Titan-XP [aka Pascal Titan-X] released. Amber 16 smashes through the half microsecond per day barrier


Intel Xeon and KNL optimizations for Amber16 released


AmberTools16 and Amber16 were released on April 30, 2016


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


Quick links

Amber force fields


Amber-related links
Benchmarks
GPU Support
Certified Hardware
File formats

Ordering Amber16
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: AmberTools16 and Amber16. You can use AmberTools16 without Amber16, but not vice versa. See below for information on how to obtain Amber16.

When citing Amber16 or AmberTools16 please use the following:

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, D.M. York and P.A. Kollman (2016), AMBER 2016, 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). Details on the ff14SB force field are here: J.A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K.E. Hauser and C. Simmerling. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J. Chem. Theor. Comput. 11, 3696-3713 (2015).

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
     
2014 - 2015
 

AmberTools16 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.

AmberTools16 (released on April 30, 2016) 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 and parmed Basic preparation programs 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 and parameter fitting
cpptraj and pytraj Structure and dynamics analysis of trajectories
MMPBSA.py and amberlite Energy-based analyses of MD trajectories

Among the new features:
  • Major update to the general Amber force field (GAFF2)
  • ff15ipq protein force field added
  • Improved support for the "12-6-4" potential model for monatomic ions.
  • Improved leaprc files for specifying which force fields to use.
  • Generation of an API for sander and cpptraj, allowing their functionality to be accessed by third-party programs. Examples include the PHENIX suite of crystallographic refinement programs, and our own new pytraj program, which supports novel ways to do trajectory analysis.
  • Significant improvments and "real-life" examples for the Low-Mode (LMOD) conformational search routines.
  • Improved workflow for system preparation and validation.
  • Periodic version of the 3D-RISM integral equation codes.
  • Codes to compute SAXS and WAXS data from MD or 3D-RISM calculations.
  • Support for the new NMR Exchange Format (NEF) formats for NMR restraints.
  • Continued updates and extensions to the cpptraj program for trajectory analysis:
    • Improved parallelization: Introduction of cross-trajectory parallelizaion and hybid MPI/Openmp
    • esander action: links to the sander API to extract energies for analysis
    • Updated nastruct and diffusion actions
    • More detailed changelog for cpptraj

  • Partial changelog for AmberTools

Changes to Amber workflows in AmberTools16:

Amber16 is now available!


We are pleased to announce the release (on April 30, 2016) of version 16 of the Amber software suite. (How to order.) This represents a significant update from version 14, which was released in April, 2014.

The Amber16 package builds on AmberTools16 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. Major new features include:

  • Semi-Isotropic Pressure Scaling (GPU)
  • Charmm VDW Force Switch (CPU, GPU)
  • Enhanced NMR Restraint support + R^6 averaging support (GPU)
  • Gaussian Accelerated Molecular Dynamics (CPU, GPU)
  • Support for external electric fields (CPU)
  • Expanded umbrella sampling support (GPU)
  • Constant pH supported with replica exchange along pH coordinate (GPU)
  • Support for gas phase MD (igb=6) (CPU, GPU)
  • Support and significant performance improvements for the latest Kepler, Maxwell and Pascal GPUs from NVIDIA.

Coming soon, via the Amber update mechanism (which is automatically run when you execute the configure script):

  • Adaptively-biased MD, now with "well-tempering" and other improvements
  • Support for Intel Knights Landing Xeon Phi on date of release.
  • Improved CPU GB performance and scaling.
  • Improved CPU PME performance and scaling.
  • Thermodynamic integration and FEP support on GPU.
  • Support for external electric fields (GPU).
  • NVIDIA Pascal GPU optimizations.
  • Support for CUDA 8.0.

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, potential of mean force (PMF), and QM/MM calculations.
     
  • 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 and parmed: 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. Parmed supports many additional manipultations.
     
  • 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 and pymsmst codes can assist in generating force fields for metal centers.
     
  • cpptraj and pytraj: 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 AmberTools16, and extacting the tar file. Parameter files will be in the amber16/dat/leap directory tree.

How to obtain the Amber16 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


San Diego, 2016

The Amber16 authors are: 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, 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: .