AMBER

Author

D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, B. Wang, D.A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J.W. Caldwell, W.S. Ross, and P.A. Kollman. Many people not listed in the author list helped add features to various codes; these contributions are described in the documentation for the individual programs.

Origin

Department of Pharmaceutical Chemistry, University of California, U.S.A.

Version

AMBER 11, 10 & 9

Official Web Site

http://ambermd.org

Brief Program Description

AMBER is an acronym for Assisted Model Building with Energy Refinement. It is a general purpose molecular mechanics/dynamics package which is designed for the refinement of macro molecular conformations using analytical potential energy function. The empirical parameters for the potential function are derived from both experimental results on smaller molecules of diverse chemical structure and ab initio quantum mechanical results on smaller molecules. These parameters have been proven to be transferable from the smaller molecules to macromolecules successfully. New parameters are constantly being developed and added to successive upgrades of the package.

The following improvements and additions have been made to the program since the previous version (AMBER11):

• 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.

• 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.

For more information on the latest features in AMBER, please visit the AMBER web site.

Areas of Application

• Conformational analysis of macro molecules

• Evaluation of redox potentials

• Site directed mutagenesis studies

• Computer modelling and drug design

• Molecular dynamics studies

• Solvation studies (solvent-macro molecule interaction)

• Enzyme catalysis studies

Implementation and Access

Amber 11 can be accessed via the command runamber11 as shown:

$CHEM/runamber11 progname [-i file] [-o file] [other options]

where progname stands for the name of one of the programs available. There are many options, details are given in the documentation.

This version runs both in serial and in parallel. For details and examples please see the man page (see below).

Please note the previous version of AMBER 10 and AMBER 9 are still available via the commands $CHEM/runamber10 and $CHEM/runamber respectively.

Machines

Available on Magellan.

Documentation

Detailed information on how to run AMBER 11 jobs may be found in the online man page, accessible by typing: man runamber11 for version 11. Previous versions for Amber 10 and 9 are still available by typing: man runamber10 and man runamber respecctively.

The AMBER 11 manual is available online in PDF format from the $CHEM/amber11/doc directory.

Tutorials are available from the AMBER web site.

Literature References

References on the methods developed and used in the package are available in the corresponding AMBER manuals.

Specialist Support

Dr Helen Tsui. Address: Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ. Tel: 020 7594 1220 Email: helen.tsui@imperial.ac.uk.

Program Restrictions and Comments

A full list of authors can be found on the front page of the AMBER 11 User's Manual.

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. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvai, 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.