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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 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.

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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

Download AmberTools

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:

  • 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.

  • 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.

  • 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.

  • A new suite of conformational clustering tools is available in ptraj.

  • 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.

  • 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.

  • 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.

Amber information

The program package

Support information

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.

CodeRelease datespeed, ps/day
Amber 4.1June, 1995103
Amber 5November, 1997104
Amber 6December, 1999121
Amber 7March, 2002135
Amber 8March, 2004179
Amber 9March, 2006249
Amber 10April, 2008314

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

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

General correspondence

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.
  • 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.

Acknowledgments

 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.

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
...photos by Guanglei Cui

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