AMBER (an acronym for Assisted Model Building and Energy Refinement) is a family of force fields for molecular dynamics of biomolecules. AMBER is also the name for the molecular dynamics simulation package.
The AMBER software suite provides a set of programs for applying the AMBER forcefields to simulations of biomolecules.
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.
-
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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