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AMBER
 
AMBER Assisted Model Building with Energy Refinement
AMBER (Assisted Model Building with Energy Refinement) 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 7.  The release consists of about 60
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.

* gibbs: This program includes free energy perturbation (FEP) and
thermodynamic integration (TI) [window growth, slow growth, and
dynamically modified windows], and also allows potential of mean
force (PMF) calculations.

* roar: This module was contributed by Ken Merz' group at Penn
State. It allows mixed quantum-mechanical/molecular-mechanical
(QM/MM) calculations, "true" Ewald simulations, and alternate
molecular dynamics integrators.

* 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. Example xleap
windows (40Kbytes of gifs). Motif-style X-windows Athena widgets
and a table widget used in LEaP were written by Vladimir
Romanovski.

* 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 and carnal: These are programs 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.

AMBER runs on Linux machines s; the executable is in:

/joule2/programs/AMBER/c28b2/exec/gnu/AMBER  or just type "AMBER"

The local documentation is in:

/joule2/programs/amber/amber7/doc/amber7.pdf 

or from the author's web site at

http://amber.scripps.edu/ 

also see tutorials:
http://amber.scripps.edu/tutorial/index.html 



NOTES FROM MIKE:

The executables will run on Linux computers.  Just type the name of the
executable.

Note1: We have the text only version of Leap, not the x-windows based
version.  The x-windows version does not compile on our Linux
machines.

Note2: Antechamber will not run because we lack the program MOPAC.
MOPAC costs $2000.