AMBER Program
by David Case and Collaborators
AMBER, by David Case at The Scripps Research Insititute and
collaborators, is the collective name for a suite of programs that allow
users to carry out molecular dynamics simulations, particularly on biomolecules.
AMBER programs
This 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. The QM/MM capability that used to be in Roar is now in sander.
- pmemd: This is an extensively-modified version (prepared by Bob Duke) of the sander program, limited to periodic, PME simulations. It is faster, and
scales better on parallel machines, than sander; hence it is usually the program of choice for "standard", periodic simulations that do not require
features it does not support.
- 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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How to run AMBER:
On chmsgi and any SGI machine that is running IRIX 6.5 or later and has chmsgi:/chem mounted you will need to modify your path and add the following line to your .cshrc file:
chmsgi:
setenv AMBERHOME /chem/AMBER/amber8_64_r14
and add to your path $AMBERHOME/exe
O2 with R5000 processors:
setenv AMBERHOME /chem/aMBER/amber8_O2_r5
and add to your path $AMBERHOME/exe
O2 with R12000 processors:
setenv AMBERHOME /chem/aMBER/amber8_O2_r12
and add to your path $AMBERHOME/exe
To run AMBER on:
k2:
add the following to your .tcshrc file:
setenv AMBERHOME /usr/local/lms/aMBER/amber8
and add to your path $AMBERHOME/exe
cosmos:
add the following to your .bash_profile file:
export AMBERHOME="/scratch/mouse/aMBER/amber8"
and add to your path $AMBERHOME/exe
Trouble-Shooting
zzz: Command not found
where zzz is one of the amber programs
The setenv command that you added to your .cshrc (.bash_profile) is either incorrect, not before the PATH line, or has not been activated yet or you have not
added $AMBERHOME to your PATH. Check the setenv line in your .cshrc file and the PATH to make sure that they match the lines given above. To activate the
modified .cshrc (.bash_profile) you may log out and log back in or simply type:
source .cshrc ( . .bash_profile)
This will activate any changes made to your .cshrc (.bash_profile) file.
