News

Quick links

Amber-related links
Benchmarks
GPU Support
Certified Hardware
File formats

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

The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses. The sander program now has the LGPL license.
AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers.
The distribution contains a Reference Manual in pdf format. You can also you can also download the PDF version of the manual, if you want to see if AmberTools might meet your needs.

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

All users need to Download AmberTools16. Use the command "tar xvfj AmberTools16.tar.bz2" to extract into a directory tree headed by amber16/. (Do not extract on top of any existing amber12 or amber14 directory trees.) Follow the installation instructions in the Reference Manual, which is in amber16/doc/Amber16.pdf.

Changes to Amber workflows in AmberTools16:

Binary output files are now the default: By default, trajectory and restart files in sander and pmemd are now written in binary (NetCDF) format. Users can use cpptraj to convert these files back to their formatted counterparts, or they can set ntxo=1 and ioutfm=0 to retain the old behavior. While we recognize that some existing scripts may need changes, we made this change for good reasons, and encourage all users to adapt their workflows to the binary file format.
There are new specifications for choosing force fields: In the past, we offered "generic" leaprc files, such as leaprc.ff14SB, which loaded a particlar combination of protein, DNA, RNA, water and ion parameters. This created a naming confusion (since only the protein part was really "ff14SB",) and made it difficult to understand how to request alternative combinations of force field parameters.
We now have separate leaprc files for proteins, DNA, RNA, water+ions, lipids and carbohydrates. Please consult Chapter 3 in the Amber 2016 Reference Manual for complete details, including our recommendations for each category. The leaprc.water.* files include suggested parameters for monatomic ions that are appropriate for the given water model. To accomplish this, some filenames for ion parameters have been changed--see the Manual, or examine the headers of the frcmod.ions* files, if you need more fine-grained control of ion parameters.
The leaprc.ff14SB has been moved to the oldff subdirectory, but is unchanged from AmberTools15. This means that it can still be used for workflows that benefit from having a "generic" leaprc file, but note that oldff/leaprc.ff14SB does not have the currently-recommended parameters for DNA, and will not be updated as other parts of force fields evolve. Users should make plans to transition away from use of files in the "oldff" subdirectory.

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

A brief description of the programs
2016 Amber Reference Manual
Bug fixes and updates
Tutorials (English)
Tutorials (Japanese translation, from Conflex Corp.)
Tutorials (Japanese translation, from Akira Wadano)
Frequently Asked Questions (FAQ)
Pretty old, but still has some useful information.
Archive of the Amber Mail Reflector
Note that this archive has a search engine linked in, so that you can easily see if your question has been asked and answered before.
Amber file formats
Table of Amber atom types

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

GPU benchmarks for the NVIDIA GPU version of Amber16 pmemd. Also contains single node CPU benchmarks.
Amber Benchmark Suite - This is a collection of benchmarks designed by Ross Walker to represent typical real world usage of Amber.
Old Benchmark timings for Amber 10. (Ross Walker SDSC).
Benchmarks from HECBioSym, (CPU only) comparing a number of MD codes (Loeffler & Wynn, March 2012, plus addendum for Amber12). Quoting from the report: "AMBER 11/pmemd fares well, especially with the smaller system sizes, and may even outperform or be on par with the other MD programs on lower core counts regardless of system size, but pmemd scales less well than GROMACS, LAMMPS or NAMD." And from the July, 2012 addendum: "AMBER 12 typically outperforms other MD packages at lower core counts on the hardware benchmarked."

Downloads

Old Prep/Link/Edit/Parm Also Spasms, a molecular dynamics program, and Resp, for charge-fitting. Resp Q&A
The Xraw widget package, which was developed for Leap by Vladimir Romanovski.
MTKPP_Examples.tar.bz2. This contains all of the example files and scripts necessary to run MCPB, as well as other illustrative examples of how to use the MTK++ library in your own programs. You should untar this file inside $AMBERHOME using, for instance the following command:
tar jxvf MTKPP_Examples.tar.bz2 -C $AMBERHOME
ncsu-umbrella-slice.tar.bz2. This contains the ncsu-umbrella-slice program necessary to recover free energies from ABMD flooding calculations.

Amber-related links

Amber-containing medicine from Poland

Tips for installing and running Amber on various architectures

Running Amber on MacOS, Linux, and Windows 10. (Short version, provided by Dave Case)
Running Amber on MacOSX, Ubuntu, Debian, openSUSE, and Windows. (Longer version, provided by Jason Swails)
Running Older versions of Amber with AmberTools13. (Provided by Jason Swails)
Running PMEMD on IBM BlueGene/L. (Provided by Bob Duke)
Running Amber on Microsoft Windows. (Provided by Thorsten Wölfle, Andreas W. Götz, Ross C. Walker and Dave Case)
Running Amber on Fujitsu Primepower and VPP systems. (Provided by Vladislav Vasilyev)
Running PMEMD on NVIDIA GPU cards.
Running Amber on the e-NMR (European NMR) grid.

Updated information about various components
More information on the antechamber module
Details on how to compute a PMF from a set of EVB simulations. (Provided by Kim Wong.)

Visualizing Amber structures and trajectories
NGLView, a lightweight trajectory viewer in Jupyter notebook , it uses pytraj/cpptraj as one of the backends.
Visual Molecular Dynamics (VMD), another Amber-aware molecular visualization package
Chimera, still another Amber-aware molecular visualization package
PCAsuite, another tool for principal component analysis of trajectories.

Related software that interfaces with Amber

System setup:
R.E.D. (RESP ESP charge derive) program, to assist and automate the process of calculating RESP charges. Prepared by A. Pigache, P. Cieplak and F.-Y. Dupradeau.
H++ is a tool to estimate pKa's of protein side chains, and to automate the process of assigning protonation states for molecular dynamics simulations.
PDB2PQR contains another tool to help prepare structures and assign protonation states of proteins.
ACPYPE is a tool based on Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN tools or ARIA. You can get this using svn:
```
svn checkout http://svn.code.sf.net/p/ccpn/code/branches/stable/ccpn/python/acpype acpype
```
Dendrimer Builder Toolkit, software which can be used to build polymer systems for simulations with Amber, from Prabal K. Maiti et al (see this reference for more details).
MemGen, a web server for setup of membrane simualtion systems, from Jochen Hub and co-workers.
Lipid construction tutorial, using the Maestro interface, from Parker de Waal.
CHARMM-GUI provides a web-based graphical user interface to generate various molecular simulation systems and input files; it supports CHARMM, NAMD, GROMACS, AMBER, and OpenMM simulation programs, mostly based on the CHARMM force fields.
Free energy analysis:
WHAM analysis: There is a new (Nov. 2007) version of Alan Grossfield's program for weighted histogram analysis.
WHAM analysis: on REMD, umbrella sampling, etc., plus tutorials for REMD in Amber. Prepared by Daniel Sindhikara, and updated Feb. 2012. rigorous kinetics using the weighted ensemble algorithm.
FESEtup, a tool to automate setup of alchemical relative free energy simulations like thermodynamic integration (TI). From Hannes Loeffler and co-workers.
Tools for alchemical analysis, assembled by the Mobley lab.
Notes from the Ryde group illustrate the use of MM-PBSA scripts, along with a new method for estimating entropies.
sietraj is an alternative to MM-PBSA for calculating binding free energies from Amber-generated MD trajectories.
Python script to simplify the computation of 3D-RISM pressure corrected (PC+/PC) hydration free energies.
Miscellaneous:
WESTPA (the Weighted Ensemble Simulation Toolkit with Parallelization and Analysis) provides a high-performance framework for carrying out extended-timescale simulations of rare events with
The SANE analysis package, for interfacing Amber with NMR processing software, provided by Brendan Duggan.
The iAPBS interface provides a way to use Amber's sander and mm_pbsa scripts to use the Adaptive Poisson-Boltzmann solver (APBS) to carry out numerical Poisson-Boltzmann calculations.
amber2accent.pl, a script that runs ptraj to extract BAT-values for use with the ACCENT-MM code of Mike Gilson's lab.
Additional analysis tools for ptraj, for diffusion, residence times, and lipid bilayer analysis, from Hannes Loeffler.
The PUPIL package allows one to carry out QM/MM MD simulations using Amber as molecular dynamics engine, among others, and a set of existing quantum mechanic programs, thus accessing to very different QM methodologies.
The PHENIX package allows one to carry out crystallographic refinement using Amber molecular mechanics force field for geometry restraints

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.

More information about Amber force fields

Glycam parameters for carbohydrates
Amber/Glycam input configurator tool, a web-based interface to help prepare inputs for sander.
Modified nucleosides for RNA, prepared by the groups of John SantaLucia and Berny Schlegel at Wayne State.
Forcefield_PTM:Amber-compatible parameters for post-translationally modified amino acids, prepared by the Floudas group at Princeton.
Zinc parameters, from Yuan-Ping Pang.
REDDB (Resp Esp charge Data Base), a database of resp charges and force field libraries for small molecules and biological molecular fragments, by P. Cieplak, F. Dupradeau and co-workers. (Hint: click on "List Projects"; "co-factor_biochemistry" has entries that are commonly requested by users.)
The ff99SBildn force field contains some modifications to ff99SB, described here: K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J.L. Klepeis, R.O. Dror and D.E. Shaw. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78:1950, 2010. To use these, download the ff99SBildn.tar file, untar it in your $AMBERHOME directory, and type "source leaprc.ff99SBildn" in your LEaP input. (Please note: The ff14SB force field adds these sorts of corrections, and many others, to ff99SB, and is now the force field that Amber developers recommend for protein simulations.)
The ff99SBnmr force field contains another set of torsional modifications for ff99SB. See D.-W. Li and R. Bruschweiler. NMR-based protein potentials. Angew. Chem. Int. Ed. 49:6778, 2010.
Contributed parameters database, maintained by Richard Bryce at the University of Manchester

Using the Amber force field in other software packages
Using the Amber force fields in Accelrys programs (via AmberFFC).
Using the Amber force field in Gaussian QM/MM calculations.
Using the Amber force field in NAMD (UIUC documentation).
Using the Amber force field in NAMD (Rutgers documentation).
Using the Amber force field in CHARMM.
Using the Amber force field in GROMACS (via ffamber).
Using the Amber force field in GROMACS (via FEsetup).
Using the Amber force field in X-plor
Using the Amber force field in MOLDEN; (see also this link.)
Using the Amber force field in desmond (Preliminary version)
Using the Amber force field in openMM
Using the Amber force field in MOE

How to obtain the Amber16 program package

Click here for the Amber 16 License Agreement. Print this form, fill it out, sign and return (with your payment) to the address given at the bottom of the license agreement.
Amber is distributed electronically; once your order is processed, you will receive download information via email. A PDF version of the Reference Manual is included in the download.
All Amber licenses are site licenses, valid for any number of users and any number of computers. You may also run Amber on computers that you do not own (e.g. at a remote computing center or in the "cloud"); see the license agreement for more information about this sort of usage.
Fees:
- Academic/non-profit/government: $500.
- Industrial (for-profit): $20,000 for new licensees, $15,000 for licensees of Amber 14. (Custom payment schedules or subscription-based approaches can be made available: please send email to <amber-admin@biomaps.rutgers.edu> for more information.)
- Porting and demonstration licenses are available, as are licenses for computing centers; see the License Agreement for details.
- (Note that no written license agreement or fee is required for AmberTools.)
Funds from licensing Amber are distributed to the institutions that employ some of the Amber authors; in this way your fees support development of new features. No money is paid directly to any of the Amber authors.
Amber is distributed in source code format, and must be compiled in order to be used. You will need Fortran 95, C and C++ compilers. You will also need to download and install AmberTools.
The academic fee may be reduced or waived in special circumstances, but a strong justification is required, and you should document a specific need for pmemd. Waivers are generally not available for researchers in North America, western Europe, or Japan. Please send a justification of your need for a waiver to amber-admin@biomaps.rutgers.edu before sending in a license form.
Payment for all orders for Amber must received prior to shipment of the Software. Payment must be via check, money order, or credit card (Mastercard/Visa/American Express). Make payments to: Regents, University of California. We are sorry, but purchase orders and wire transfers can no longer be accepted.
Do not send credit card information via email. This is not secure and could cause account theft. Please send credit card information only by way of fax, mail, or phone.
People who licensed Amber 14 after February 1, 2016 are eligible for a free upgrade to Amber 16 when it is released. (This is not automatic: if you wish to obtain the new version, you need fill out and submit a license form, indicating that you are eligible for the upgrade.)

General correspondence

Please direct administrative correspondence about Amber (including queries about interpreting the license agreement, reflector problems, etc.) to: amber-admin@biomaps.rutgers.edu.
Administrative questions about obtaining Amber (e.g. payment details, delays in receiving your copy) should be addressed to Alma Rosa Agorilla at the address below.
Scientific questions about installing or using Amber should go to: amber@ambermd.org. This mail will be forwarded to all those subscribed to the Amber reflector, and hence, many people may be able to help out. In order to post questions, you must first subscribe to the list: send a blank email to amber-subscribe@ambermd.org. Additional information about the AMBER mail reflector can be found at http://lists.ambermd.org/mailman/listinfo/amber
Amber contact information for licensing:

Alma Rosa Agorilla
AMBER Software Administrator; MC2280
University of California, San Francisco
600 16th St. Room 518B
San Francisco, CA 94143-2280
Phone: (415) 514-3647
Fax: (415) 390-9174
email: AMBER-Users@ucsf.edu
Do not send credit card information via email. This is not secure and could cause account theft. Please send credit card information only by way of fax, mail, or phone.

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:

amber@ambermd.org

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

Athens, Georgia, 2017

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

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