Amber

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Description

Program Amber is a set of molecular mechanical force fields for the simulation of biomolecules (biologically important macromolecules – especially proteins and nucleic acids) The program package is created by package of molecular simulation programs, computings of molecular mechanics, simulation of molecular dynamics with tools for analyze and visualization results (program Moil-View).

Program package contains cca 50 programs, which cover wide spectrum of computational chemistry. Main programs are following Amber modules:

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 (before was in module roar

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.

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.

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: TThis 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.

Availability

The following versions are available:

  • 14.0 (modules amber-14 and amber-14-gpu)
    • version available for all the MetaCentrum and CERIT-SC users
    • variant amber-14 is compiled by Intel compiler with the support of Intel MKL and distributed (MPI) computing (OpenMPI)
    • variant amber-14-gpu is compiled by Intel compiler with the support of Intel MKL, GPU computing (CUDA 6.0), and distributed (MPI) computing (OpenMPI)
  • 10 and 12 (in the appropriate modules --- amber10, amber-12)
    • version 12 is available just for the Masaryk University users
    • furthermore, special parallel versions are available based on the module suffix, e.g.:
      • shmem: parallel version using MPI above shared memory (for single machines with more processors) (module amber8-mpich-shmem)

Use

Load the appropriate Amber package based on the desired version (e.g., module add amber-14) and run the desired program in accordance with its documentation.

Documentation

on-line documentation is available.

Licence

  • Amber v. 14 is licensed for all the MetaCentrum and CERIT-SC infrastructure users
  • Amber v. 10 is licensed for all the UK a UJP students/employees.

Supported platforms

SGI Irix, Linux, IBM AIX, HP Unix, Sun OS, Max OS, MS Windows (with use program Cygwin), MD-GRAPE

Program manager

meta@cesnet.cz

Homepage

URL: http://ambermd.org/, http://www.emporia.edu/

Example

$ qsub -l nodes=2:ppn=4:x86_64,mem=1gb -q normal job.sh

where job.sh follows (lojza is login)

#!/bin/sh
#
# name of job
#PBS -N job
#
# messaging of end of job
#PBS -m ae
#
# one file for output and error (from PBS we get file job.o<number of job>)
#PBS -j oe
#
# copy the Amber's input data from a shared NFSv4 storage to a scratch volume
cp /storage/brno2/home/$USER/job.in $SCRATCHDIR
#
# change the working directory
cd $SCRATCHDIR || exit 1
#
# adding of module
module add amber14
#
# run of computation
mpirun sander.MPI -O -i ./job.in  -c molekula  -o ./job.output
#
# copy out the Amber's output data to a shared NFSv4 storage
cp job.output /storage/brno2/home/$USER/
#
# clean the temporary storage
rm -rf $SCRATCHDIR