Preinstalled Amber Certified
GPU Workstations and Clusters now available with GTX-780, GTX-Titan-Black,
K20 and K40
AmberTools14 and Amber14 were released on April 15, 2014
Aug 2013, GTX-780 and Titan GPUs now officially supported. Updated benchmarks and recommended hardware available.
Amber force fields
The AMBER community congratulates Martin Karplus,
Michael Levitt and Arieh Warshel
on the award of the 2013 Nobel Prize in chemistry.
Assisted Model Building with Energy
"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
simulation programs which includes source code and demos.
Amber is distributed in two parts:
AmberTools14 and Amber14. You
can use AmberTools14 without Amber14, but not vice versa. See below for information on how to obtain Amber14.
When citing Amber14 or AmberTools14 please use the following:
D.A. Case, V. Babin, J.T. Berryman, R.M. Betz, Q. Cai, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, H. Gohlke, A.W. Goetz, S. Gusarov, N. Homeyer, P. Janowski, J. Kaus, I. Kolossváry, A. Kovalenko, T.S. Lee, S. LeGrand, T. Luchko, R. Luo, B. Madej, K.M. Merz, F. Paesani, D.R. Roe, A. Roitberg, C. Sagui, R. Salomon-Ferrer, G. Seabra, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu and P.A. Kollman (2014), AMBER 14, 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).
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
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,
Amber developers, January 2014
AmberTools14 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.
AmberTools14 (released on April 15, 2014) consists of the following main codes:
||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|
||Basic preparation program for Amber simulations|
||semiempirical and DFTB quantum chemistry program|
||Performs numerical solutions to Poisson-Boltzmann models|
||Solves integral equation models for solvation|
||Workhorse program for molecular dynamics simulations|
||Explicit solvent molecular dynamics simulations|
|ptraj and cpptraj
||Structure and dynamics analysis of trajectories|
|MMPBSA.py and amberlite
||Energy-based analyses of MD trajectories|
The programs here 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,
- 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 in AmberTools14:
A more detailed changelog can be found here
- The sander module, our workhorse simulation program, is now a part
- Greatly expanded and improved cpptraj program for analyzing
- new documentation and tools for inspecting and modifying Amber
- Improved workflow for setting up and analyzing simulations;
- new capability for semi-empirical Born-Oppenheimer molecular dynamics;
- EMIL: a new absolute free energy method using TI;
- New Free Energy Workflow (FEW) tool automates free energy calculations (LIE,
TI, and MM/PBSA-type calculations);
- Completely reorganized Reference Manual
- All users need to Download
AmberTools14. This tar file will extract into a directory named
amber14. Follow the installation instructions in the Reference
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 major differences include:
Force fields: Amber has two new fixed-charge protein force fields,
ff14SB and ff14ipq, a new modular lipid force field,
Lipid14, and updates to nucleic acid and carbohydrate force fields.
Improved options for self-guided Langevin dynamics and accelerated
molecular dynamics, to enchance sampling along soft degrees of freedom.
A completely reorganized Reference Manual
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 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
Support is also included for the latest Kepler, Titan and
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, and a new
absolute free energy method.
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.
The release consists of about 50 programs, that work reasonably well
together. The major programs are as follows:
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
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
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 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.
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
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
- Benchmark timings for Amber 10.
(Ross Walker SDSC).
- Benchmark timings for Amber 11. (MS Windows PMEMD - Thorsten Wölfle, Andreas Götz, Ross Walker: SDSC)
- GPU benchmarks for the NVIDIA version
of Amber12 pmemd.
- Amber Benchmark Suite
- This is a collection of benchmarks designed by Ross Walker to represent
typical real world usage of Amber.
from Daresbury, comparing a number of MD codes (Loeffler & Wynn, March
2012). 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."
- Old Prep/Link/Edit/Parm Also Spasms, a molecular
dynamics program, and Resp, for charge-fitting.
- The Xraw widget package,
which was developed for Leap by Vladimir Romanovski.
- Cellulose benchmark, for timings on
a "largish" system with 408,000 atoms.
- AmberTools, version 13. This
is for people who have Amber12 and do not have version 13 of AmberTools. Untar
this file into your amber12 tree, and follow the installation instructions in
amber12/doc/AmberTools.pdf. Note: Keep newer versions of AmberTools in
a separate directory tree.
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
This contains the ncsu-umbrella-slice program necessary to recover free
energies from ABMD flooding calculations.
Tips for installing and running Amber on various architectures
- Running Amber on Ubuntu, Fedora, or SUSE Linux.
- Running Amber on MacOSX,
Ubuntu, Debian, openSUSE, and Windows. (Provided by Jason Swails)
Older versions of Amber with AmberTools13. (Provided by Jason Swails)
- Running PMEMD on IBM BlueGene/L.
(Provided by Bob Duke)
- Running Amber on Sun OS. (Provided by Scott
- 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)
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
Display, a lightweight, Amber-aware trajectory viewer
- Visual Molecular
Dynamics (VMD), another Amber-aware molecular visualization package
still another Amber-aware molecular visualization package
- IED, (Interactive
Dynamics) allows analysis and visualization of essential dynamics (aka
quasiharmonic) and normal mode results.
another tool for principal component analysis of trajectories.
- DNA plotting
tools, from Stephane Teletchea, shows how to create helicoidal plots from
Related software that interfaces with Amber
- 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.
- Multiscale Modeling Tools in
Structural Biology (MMTSB) can be used for replica exchange calculations
with sander. This package also facilitates other Amber
tasks, such as dealing in a consistent way with an ensemble of
conformations, massaging PDB files, and carrying out some common types of
- 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.
- WHAM analysis: There is
a new (Nov. 2007) version of Alan Grossfield's program for weighted histogram
WHAM analysis: on REMD, umbrella sampling, etc., plus tutorials for REMD
in Amber. Prepared by Daniel Sindhikara, and updated Feb. 2012.
- The SANE analysis package, for interfacing
Amber with NMR processing software, provided by Brendan Duggan.
- sietraj is
an alternative to MM-PBSA for calculating binding free energies from
Amber-generated MD trajectories.
- The PLUMED package
contains plugins to carry out free energy simulations with Amber (and with
other molecular dynamics packages).
- Notes from the
Ryde group illustrate the use of MM-PBSA scripts, along with a new method
for estimating entropies.
- 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.
- 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.
- 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.
- 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).
- 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 force field
Note: All Amber force field parameter files can be obtained by
downloading AmberTools14, and extacting
the tar file. Parameter files will be in the amber14/dat/leap
More information about Amber force fields
Glycam parameters for
configurator tool, a web-based interface to help prepare inputs for
nucleosides for RNA, prepared by the groups of John SantaLucia and Berny
Schlegel at Wayne State.
parameters for post-translationally modified amino acids, prepared by the
Floudas group at Princeton.
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.
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.
parameters database, maintained by Richard Bryce at the University of
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.
Amber force field in NAMD (UIUC documentation).
Amber force field in NAMD (Rutgers documentation).
Using the Amber force field in CHARMM.
Amber force field in GROMACS (via ffamber).
Amber force field in GROMACS (via acpype).
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
Using the Amber force
field in openMM
Using the Amber force
field in MOE
How to obtain the Amber14 program package
Click here for the
Amber 14 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 now distributed electronically; once your order is processed,
you will receive download information via email. PDF versions of the
Reference Manual are included in the download.
Industrial (for-profit): $20,000 for new licensees, $15,000 for
licensees of Amber 12.
Porting and demonstration licenses are available, as are licenses for
computing centers; see the License Agreement for details.
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
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 license Amber 12 after February 15, 2014 are eligible for
a free upgrade to Amber 14. (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.)
- Please direct administrative correspondence about Amber
(including queries about interpreting the license agreement,
reflector problems, etc.) to:
- Administrative questions about obtaining Amber (e.g. payment
details, delays in
receiving your copy) should be addressed to Nicole A. T. Flowers at the address
- Scientific questions about installing or using Amber should go to:
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
information about the AMBER mail reflector can be found at
Amber contact information for licensing:
Nicole A. Takesono Flowers
AMBER Software Administrator
CCB Graduate Program; MC 2280
University of California, San Francisco
600 16th St. Room 522
San Francisco, CA 94158-2517
Phone: (415) 502-6518
Fax: (415) 514-1546
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
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:
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, firstname.lastname@example.org. 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 is developed in an active collaboration of
at Rutgers University,
Tom Cheatham at
the University of Utah,
Ken Merz and
Adrian Roitberg at Florida,
Carlos Simmerling at
Ray Luo at UC Irvine,
Wang at UT Southwestern,
Ross Walker at UC San Diego, and
Amber was originally developed under the leadership of
The photo at the left shows the Amber crew at its October, 2004 meeting in
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,
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
Salt Lake City, 2013
Stony Brook, January 2014
The Amber14 authors are:
D.A. Case, V. Babin, J.T. Berryman, R.M. Betz, Q. Cai, D.S. Cerutti, T.E. Cheatham, III,
T.A. Darden, R.E. Duke, H. Gohlke, A.W. Goetz, S. Gusarov, N. Homeyer, P.
Janowski, J. Kaus, I. Kolossváry, A. Kovalenko, T.S. Lee, S. LeGrand, T.
Luchko, R. Luo, B. Madej, K.M. Merz, F. Paesani, D.R. Roe, A. Roitberg, C.
Sagui, R. Salomon-Ferrer, G. Seabra, C.L. Simmerling, W. Smith, J. Swails,
R.C. Walker, J. Wang, R.M. Wolf, X. Wu 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