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 10, which is distributed by UCSF
subject to a licensing agreement described
below.
Amber is now distributed in two parts:
AmberTools and Amber10. You
can use AmberTools without Amber10, 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).
When citing Amber Version 10 in the literature please use the following citation:
D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo,
M. Crowley, Ross C. Walker,W. Zhang, K.M. Merz, B.Wang, S. Hayik, A. Roitberg, G. Seabra, I.
Kolossváry, K.F.Wong, F. Paesani, J. Vanicek, X.Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke,
L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin,
and P.A. Kollman (2008), AMBER 10, University of California, San Francisco.
AmberTools 1.2 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
mechanics investigations (using NAB), but which are restricted to gas-phase or
generalized Born solvent models.
AmberTools currently consists of four main codes that were previously
released separately, and one new one:
nucleic acid builder (NAB) |
http://casegroup.rutgers.edu/nab.html |
antechamber |
http://ambermd.org/antechamber |
ptraj |
http://www.chpc.utah.edu/~cheatham/software.html |
tleap and xleap |
http://ambermd.org |
sleap |
New: replaces and expands tleap |
- We expect that AmberTools will be dynamic, and change and grow over time.
This initial release consists of programs that have previously been part of
Amber (including LEaP, antechamber and ptraj), along with NAB (Nucleic Acid
Builder), which has been released separately. Each of these packages (except
for sleap) has been in use for a long time. They are certainly not
bug-free, but you should be able to rely upon them in many circumstances.
These are the latest releases of these programs, and collect in one place
codes that we have been distributing for some time.
-
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 and C++ compilers, plus g77 or gfortran if
you wish to compile the Mopac program.
- 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
purchase a bound copy of the Users'
Manual from lulu.com. Cost is 13.50 USD (plus shipping) per copy. (The Amber developers
take no profit or commission from such sales.)
- NAB was developed with support from the NIH Research Resource on
Multiscale Modeling Tools for
Structural Biology.
- Version 1.1 (July, 2008) is a bug-fix release, that also allows compilation on
more systems. It incorporates bugfixes 1-7, plus some other fixes. Version
1.2 (also July, 2008) adds in some fixes to the mopac routines to provide
better SCF convergence.
Amber 10 is now available!
We are happy to announce the release (on April 14, 2008) of version 10 of
the Amber software suite.
(How to order.)
This represents a significant update from version
9, which was released in March, 2006. The major differences include:
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Force fields: Many new force field types are available, including
new water and ion models; updated nucleic acid and carbohydrate parameters;
parallel support for the AMOEBA polarizable potentials of Ren and Ponder; and
improved empirical valence bond (EVB) models that can be used to construct
approximate potentials for chemical reactions.
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QM/MM Simulations: Amber 10 now allows DFTB calculations in periodic
solvent boxes or with the generalized Born solvation model. Codes are faster
and (modestly) parallel.
-
Adaptively biased simulations can be used to accelerate sampling and free
energy convergence.
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Path integral molecular dynamics simulations can be used to sample
equilibrium canonical distributions using quantum dynamics rather than
Newton's equations for nuclear motion. Both equilibrium and kinetic isotope
effects can be estimated via thermodynamic integration over mass. Rate
constants can be estimated using the Quantum Instanton model, and approximate
quantum time-correlation functions are available using Ring Polymer MD or
Centroid MD.
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A new suite of conformational clustering tools is available in ptraj.
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New free energy tools significantly simplify the setup of mutational
changes in proteins, allowing for both "single" and "dual" topologies.
A soft-core potential facility aids
sampling in systems where atoms are appearing or disappearing, with no need
for the creation of artificial dummy atoms.
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Updates to the replica exchange methods, including improvements to
the standard replica exchange code and support for exchange methods with a
non-Boltzmann reservoir, or in which a hybrid solvent model is used to reduce
the number of replicas required for large systems in explicit solvent.
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Significant improvements in speed and parallel scaling are available
in an expanded pmemd program, which now includes generalized Born
capability, and support for off-center charges (as in TIP4P or TIP5P).
- Full integration of the low-mode (LMOD) search tools based on
following low-frequency normal modes.
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Amber information
The program package
Support information
- Tutorials (English) (updated, September, 2008)
- Tutorials (Japanese)
- Frequently Asked Questions (FAQ)
- 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.
There is also a backup of the reflector archive hosted by Jarrod Smith and Vanderbilt.
- Selected responses from the Amber Reflector
- Amber file formats
- Benchmark timings for Amber 8
- Benchmark timings for Amber 9 PMEMD.
(Contributed by Bob Duke, for a wide variety of machines).
- Benchmark timings for Amber 9 PMEMD.
(Contributed by Ross Walker, for machines at the San Diego Supercomputer
Center).
- Benchmark timings for Amber 10.
(Ross Walker SDSC) - This includes a new more realistic benchmark suite as well as newer machines.
- 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.
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 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(!).
The parallel scaling of Amber has also improved a lot recently, but that is
another story....
Amber-related links
Tips for running Amber 8 or 9 on various architectures
(These pages may also provide some useful hints if you are having troubles
with Amber 10.)
- Running Amber 9 on San Diego Supercomputer Center's Machines
(Datastar, Teragrid & Bluegene). (Provided by Ross Walker)
- Running Amber 9 on Mac OSX
(Power PC and Intel). (Provided by Mengjuei Hsieh)
- Running PMEMD 9 on IBM BlueGene/L.
(Provided by Bob Duke)
- Running Amber 9 on a ClearSpeed Advanced Accelerator Board. (Provided by Ingvar Lagerstedt of ClearSpeed).
- Running Amber on Sun OS. (Provided by Scott
Brozell)
- Running Amber on Microsoft Windows.
(Provided by 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)
- Tips for configuring Amber 8 are here.
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.
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.
- The SANE analysis package, for interfacing Amber with NMR processing
software, is available here. Thanks to Brendan
Duggan for making this available.
- sietraj is
an alternative to MM-PBSA for calculating binding free energies from
Amber-generated MD trajectories.
The force field
Who to contact for more information...
How to obtain the Amber program package
Click here for the
Amber 10 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 9.
Porting and demonstration licenses are available; see the License Agreement
for details.
Notes
-
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 9 after February 1, 2008 are eligible for
a free upgrade to Amber 10. 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 14.60 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
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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.
The Amber programs
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 (prepared by Bob Duke) of the
sander program, optimized for periodic, PME simulations, and for GB
simulations. It is faster, and
scales better on parallel machines, than sander; 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.
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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.
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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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Acknowledgments
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Amber is developed in an active collaboration of
David Case
at Rutgers University,
Tom Cheatham at
the University of Utah,
Tom Darden at NIEHS,
Ken Merz at Florida,
Carlos Simmerling at
SUNY-Stony Brook,
Ray Luo at UC Irvine,
and Junmei
Wang at Encysive Pharmaceuticals.
Amber was originally developed under the leadership of
Peter Kollman, and Version 9 is dedicated to his memory.
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 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' Meeting on St. Simon
Island, Georgia.
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The Amber 10 authors are:
D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling,
J. Wang, R.E. Duke, R. Luo, M. Crowley, R. C. Walker, W. Zhang, K.M. Merz,
B. Wang, S. Hayik, A. Roitberg,
G. Seabra, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, X. Wu,
S. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan,
V. Hornak, G. Cui, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin,
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.
Amber developers at work |
Amber developers at play |
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| ...photos by Guanglei Cui |
Last modified:
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