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 10 & AMBER 9 |
Official Web Site |
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. Features in AMBER 9: Force fields Many new force fields are available: - updates to existing non-polarizable (f99) and polarizable (ff02) protein force fields, with improved torsional parameters for peptides and proteins - a new united-atom (no non-polar hydrogens) force field - an extension of the General Amber Force Field (gaff) that expands the range of applicable molecules, particularly for conjugated systems - support for the AMOEBA polarizable potentials of Ren and Ponder - an empirical valence bond model that can be used to construct approximate potentials for chemical reactions QM/MM Simulations Amber 9 features new and significantly improved QM/MM support. The QM/MM facility supports gas phase, implicit solvent (GB) and periodic boundary (PME) simulations where the energies and forces for the QM part of the system can be derived from a semi-empirical method, such as MNDO, AM1, PM3, or PM3/PDDG. Compared to earlier versions, the QM/MM implementation offers improved accuracy, energy conservation, and performance. Generalized Born (GB) models Amber 9 features a new model with a pairwise molecular volume correction that shows substantially better agreement with molecular surface Poisson- Boltzmann and explicit solvent results than previous Amber GB models. Updates to the Poisson-Boltzmann applications These include new nonbonded routines, newly optimized atomic cavity radii based on explicit-solvent free energy simulations, improved visualization option for electrostatic potential, and a new nonpolar solvation model with an explicit treatment of dispersion interaction that greatly improves the correlation with nonpolar solvation free energies in explicit solvent. Nudged elastic band simulations These can be used to search for approximate transition states in complex transformations. The self-guided Langevin dynamics method can be used to accelerate conformational searches. Path integral molecular dynamics simulations These can be used to sample equilibrium canonical distributions using quantum dynamics rather than Newton's equations for nuclear motion. Free energies Free energies can be estimated from from non-equilibrium "targeted" or "pulling" simulations, using the Jarzynski identity. Replica exchange methods Improvements have been made to the standard replica exchange code and there is now support for a new replica exchange method in which a hybrid solvent model is used to reduce the number of replicas required for large systems in explicit solvent. New features in AMBER 10: Force fields Many new force fields are available: - new water and ion models - updated nucleic acid and carbohydrate parameters - parallel support for the AMOEBA polarizable potentials of Ren and Ponder - improved empirical valence bond (EVB) models that can be used to construct approximate potentials for chemical reaction 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 These can be used to accelerate sampling and free energy convergence. Path integral molecular dynamics These 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. Conformational clustering tools A new suite of conformational clustering tools is available in ptraj. Free energy tools 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. Replica exchange methods 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 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). Low-mode search tools (LMOD) Full integration of the low-mode (LMOD) search tools based on following low-frequency normal modes. For more information on the latest features in AMBER, please visit the AMBER web site. AMBER consists of a suite of programs for molecular modelling and molecular simulations, each of which is designed to carry out a specific task. They can be classified into three categories:
Each program has its own unix interface and its own set of options, of which many cannot be used for the other programs. All the options provided by the user for a particular program are picked up by the $CHEM/runamber10 command for AMBER 10 and $CHEM/runamber command for AMBER 9 and submitted to that program. Any files specified by the various options for input are expected by the command to be in the user's current directory. Similarly, all the output files requested by the various options will also be deposited there. Data for the Calculations All data provided for the calculations is in the directory: /usr/local/Chem-Apps/amber10/dat for AMBER 10 The descriptions of the data is in this directory in the 0README file. Pre-processors LEaP is a special interactive preprocessor that helps in setting up the input data. It should be noted that LEaP can be used both in command mode (where one types in the commands at the prompt) or in X-mode, where one works in a special X-window designed to help to edit and examine the system of interest in a full screen environment. ANTECHAMBER is the main program from the Antechamber suite. If your system contains more that just standard nucleic acids or proteins, this may help you prepare the input for LEaP. Simulation programs The programs available are:
Post-processors There are a number of programs provided for the analysis of the output data from MD runs. These include:
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Areas of Application |
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Implementation and Access |
AMBER is implemented on Magellan. Access is via the command for version 10 runamber as shown: $CHEM/runamber10 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 that AMBER 9 is still the default version and it can be accessed via the command: $CHEM/runamber. |
Machines |
Available on Magellan. |
Documentation |
Detailed information on how to run AMBER jobs may be found in the online man page, accessible by typing: man runamber10 for version 10 and man runamber for the default version AMBER 9. The AMBER manual is available online in PDF format from the $CHEM/amber9/doc directory for version 9 and $CHEM/amber10/doc for version 10. 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 |
For information on the AMBER file formats and descriptions, force field equation and parameter files, please visit the AMBER web site. |