News
NVIDIA announces MD SimCluster Project
Major performance update to GPU accelerated PMEMD released
AmberTools version 1.5 is released
Updated version of amberlite
MPI Multi-GPU Accelerated MD
NVIDIA CEO highlights AMBER GPU port
Windows binaries
Quick links
Amber force fields
Amber-related links
Benchmarks
GPU Support
File formats
Ordering Amber11
Mailing lists
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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. The
current version of the code is
Amber version 11, which is distributed by UCSF
subject to a licensing agreement described
below.
Amber is distributed in two parts:
AmberTools (version 1.5) and Amber11. You
can use AmberTools without Amber11, but not vice versa.
A good general overview of the Amber codes can be found in:
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 11 and AmberTools 1.5 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.P. Roberts, B. Wang, S. Hayik, A. Roitberg,
G. Seabra, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, 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, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and
P.A. Kollman (2010), AMBER 11, University of California, San Francisco.

Amber developers, January 2012
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AmberTools 1.5 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 (non-periodic) molecular dynamics
simulations (using NAB), with
generalized Born solvent models. New to version 1.5 are:
- MMPBSA.py, a much-expanded program for energetic analyses of trajectories
- amberlite, a simplified interface for mm-pbsa analyses of protein-ligand
interactions
- MCPB, a platform for developing parameters for active sites of
metalloproteins
- cpptraj, an expanded trajectory analysis program
- mdgx, a coding platform for explicit-solvent MD simulations
- updates to GAFF (general Amber force field) and to the RNA force fields
AmberTools 1.5 consists of seven main codes that were previously
released separately, and five new ones:
| 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 sleap |
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 |
| 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,
licenses.
- AmberTools is distributed in source code format, and must be compiled in
order to be used. You will need C, C++ and Fortran90 compilers.
- We
hope to add new functionality to AmberTools as additional programs become
available. If you have suggestions for what might be added, please contact us.
- The download contains a Users' 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.
Or you can purchase
a bound copy of the manual; (this is sold at cost: Amber developers take
no profit or commission from these sales.)
- Most returning users will want to install version 1.5 in the same
location as ("on top of") an existing AmberTools 1.4 directory tree. If you
do this, please:
- Keep a backup copy of your current amber11 tree, in case
something goes awry;
- Be sure to "make clean" and re-run the configure script in the
amber11/AmberTools/src directory. Follow its instructions about
running the AT15_Amber11.py script before recompiling Amber itself.
Amber 11 is now available!
We are happy to announce the release (on April 25, 2010) of version 11 of
the Amber software suite.
(How to order.)
This represents a significant update from version
10, which was released in April, 2008. The major differences include:
-
Force fields: Amber now supports most CHARMM fixed-charge force fields,
including those with CMAP torsional potentials. There is also an updated
version of GAFF, the general Amber force field for organic molecules.
-
A new parameterization of the generalized Born solvation model is
available, optimized for peptides and proteins.
-
Expanded options exist for numerical Poisson-Boltzmann solvation
calculations.
-
Solvation effects can also be estimated using a 3D-RISM integral equation
model, using the Kovalenko-Hirata (and other) closure approximations.
-
There is improved integration with the Chimera visualization program,
and with UCSF DOCK.
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-
Simplified methods are available for free energy calculations that change
Hamiltonian models, including better procedures for appearing and disappearing
atoms.
-
Amber 11 includes a new implementation of the nudged elastic band model
for finding low-energy pathways for conformational transitions, which can be
used for only part of the system, or in explicit solvent simulations.
-
There are updated scripts for constant pH simulations and for
MMPB/SA free energy calculations.
-
The "polar" version the isotropic periodic sum model has been added,
along with its IPS-DFFT counterpart.
-
MD simulations using pmemd can take advantage of NVIDIA GPU
cards to obtain significant speedups compared to traditional CPU codes.
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General information
|
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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
with version 11 it includes NVIDIA GPU acceleration; hence it is generally the
program of choice, unless you need options that it does not support.
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.
- nmode:
Normal mode analysis program using first and second derivative
information, used to find search for local
minima, perform vibrational analysis, and search for transition
states.
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-
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.
-
ptraj:
This is 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:
This is a script to 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.
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Benchmarks
Downloads
- Old Prep/Link/Edit/Parm Also Spasms, a molecular
dynamics program, and Resp, for charge-fitting.
Resp Q&A
- Replica exchange (REM) test suite
for Amber 8. This was inadvertently left out of the distribution. Untar this
file in your $AMBERHOME/test directory. Not needed for Amber 9.
- The Xraw widget package,
which was developed for Leap by Vladimir Romanovski.
- Cellulose benchmark, for timings on
a "largish" system with 408,000 atoms.
- amber2accent.pl, a script that runs ptraj to extract BAT-values for use with the ACCENT-MM code of Mike Gilson's lab.
- AmberTools, version
1.2. This is for people who have Amber10 and do not have version
1.2 of AmberTools. Untar this file into your amber10 tree, and follow
the installation instructions in amber10/doc/AmberTools.pdf.
Note: Keep versions 1.3 or 1.4 of AmberTools in a separate, amber11
directory tree.
Amber-related links
Tips for running Amber on various architectures
- Running Amber on NSF TeraGrid Machines
- Running Amber on Mac OSX
(Power PC and Intel). (Provided by Mengjuei Hsieh)
- Running Amber on Ubuntu Linux. (Provided by Scott
Brozell)
- Running PMEMD on IBM BlueGene/L.
(Provided by Bob Duke)
- Running Amber on Sun OS. (Provided by Scott
Brozell)
- Running Amber on Microsoft Windows.
(Provided by Thorsten Wölfle, Andreas W. Götz, Ross C. Walker and Dave Case)
- Running Amber on
MD-GRAPE hardware
from RIKEN. (Provided by Tetsu Narumi at RIKEN)
- 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.)
- Patches for the
NPSA
implicit solvent model from Rebecca Wade's group.
- Patches for the
Random acceleration MD (RAMD) method, also from Rebecca Wade's group.
-
Extra ptraj routines to compute diffusion properties, residence times and
distances to nearest neighbor boxes.
Visualizing Amber structures and trajectories
- MOIL-View: an Amber and LES-aware molecular graphics package
- MD
Display, a lightweight, Amber-aware trajectory viewer
- Visual Molecular
Dynamics (VMD), another Amber-aware molecular visualization package
- Chimera,
still another Amber-aware molecular visualization package
- IED, (Interactive Essential
Dynamics) allows analysis and visualization of essential dynamics (aka
quasiharmonic) and normal mode results.
- DNA plotting
tools, from Stephane Teletchea, shows how to create helicoidal plots from
Amber trajectories.
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
structural analysis.
- 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
analysis.
- Modular reweighting
software for statistical mechanical analysis of biased
equilibrium data, with Amber examples, prepared by Daniel Sindhikara.
- 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 Amber11 (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.
The force field
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.
- 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.
- 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.
- 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 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
(Preliminary version)
- Using the Amber force
field in openMM
How to obtain the Amber11 program package
-
Click here for the
Amber 11 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 Users'
Manual are included in the download, and you can order bound copies of the
manual from LuLu Press.
-
Fees:
Academic/non-profit/government: $400.
Industrial (for-profit): $20,000 for new licensees, $15,000 for
licensees of Amber 10.
Porting and demonstration licenses are available; 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. 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 10 after January 15, 2010 are eligible for
a free upgrade to Amber 11. This is not automatic: if you
wish to obtain the new version, please fill out and submit the license form,
indicating that you are eligible for the upgrade.
- The distribution contains a Users' Manual in pdf format. You can also
purchase a bound copy of the Users'
Manual from lulu.com. Cost is 14.50 USD (plus shipping) per copy. (The Amber developers
take no profit or commission from such sales.) Click here for updates and corrections to the printed
manual.
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 Nicole A. T. Flowers 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:
-
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
email: nicole@picasso.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
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.


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St. Simon Island, 2009

Stony Brook, 2010

Athens, Georgia, 2011

Rutgers, 2012
The Amber 11 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, B. Wang, S. Hayik, A.
Roitberg,
G. Seabra, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, 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, 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.
Research support from DARPA, the NIH, and the NSF for Peter Kollman is
gratefully acknowledged, as is support from the NIH, ONR and DOE for
David Case. Use of the facilities of the UCSF Computer Graphics
Laboratory (Thomas Ferrin, PI) is appreciated.
Scott Brozell acknowledges the use of computational facilities at the
Ohio Supercomputer Center.
NAB was developed with support from the NIH Research Resource on
Multiscale Modeling Tools for
Structural Biology.
| Amber developers at work |
Amber developers at play |
 |
   |
A trip down memory lane
Here are some timings for a
standard Amber benchmark, but over about a decade of code changes. The
benchmark is "jac", which is dihydrofolate reductase (159 residue protein) in TIP3P
water (23,558 total atoms). PME is used for electrostatics, and van der Waals
interactions are truncated at 9 Ang.
The table shows speeds for running 1000 steps (with a time step of 1 fs)
on a single cpu (Intel Xeon
x86_64, 3.4 GHz). All codes were compiled with the Intel ifort compiler,
version 9.0.
Notes: Amber 4.1 and 5 required one to force frequent list updates in
order to conserve energy, and such timings are shown below; using default
parameters for those codes give timings about equal to Amber 7.
Versions 6-10 give identical results for this test, up to roundoff errors.
Timings for versions 4.1 to 7 are for sander, those for versions 8 to
10 are for pmemd.
| Code | Release
date | speed, ps/day |
| Amber 4.1 | June, 1995 | 103 |
| Amber 5 | November, 1997 | 104 |
| Amber 6 | December, 1999 | 121 |
| Amber 7 | March, 2002 | 135 |
| Amber 8 | March, 2004 | 179 |
| Amber 9 | March, 2006 | 249 |
| Amber 10 | April, 2008 | 314 |
So, the current code is more than twice as fast as it was 6 years ago.
These numbers don't factor in changes in hardware speed. As one point of
reference, my (DAC) desktop computer in 2000 was an SGI 250MHz R10000 machine.
That machine, using Amber 6, ran this benchmark at a speed of 12 ps/day(!).
On the other end, in 2010, a single Tesla C2050 GPU card runs this benchmark
at over 11
ns/day (more information is here).
The parallel scaling of Amber has also improved a lot recently, but that is
another story. As a simple example, this benchmark runs at 4.9 ns/day on a
single (dual-quad) node "Nehalem" workstation (X5570, 2.93 GHz).
Last modified:
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