Amber

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.

License

• Amber v. 22 is licensed for all UK and MUNI students/employees.
• Amber v. 18 is licensed for all UK students/employees.
• Amber v. 14 is licensed for all the MetaCentrum and CERIT-SC infrastructure users
• Amber v. 10 is licensed for all UK and UJP students/employees.

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of amber and load default version of amber as

module avail amber/ # list available modules
module load amber   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail amber

and choose explicit version you want to use.

• 22.0 (modules amber/22)
  • version available only for Charles University and Masaryk University students and employees.
  • The module contains all types of binaries - sequential, .MPI, .OMP and .cuda (GPU).
• 18.0 (modules amber-18)
  • version available only for Charles University students and employees.
  • variant amber-18-intel compiled by Intel Compiler with OpenMPI support (.MPI suffixes), including pmemd.gem (preferred non-GPU variant)
  • variant amber-18 compiled by GCC with OpenMPI support (.MPI suffixes)
  • variant amber-18-gpu-upd17 activates binaries for GPU version (update 17) compiled by IntelCDK with OpenMPI parallel support (.cuda and .cuda.MPI suffixes)
  • variant amber-18-gpu activates binaries for GPU version (update 14) compiled by IntelCDK with OpenMPI parallel support (.cuda and .cuda.MPI suffixes), does not support GPUs with CUDA capability 8.0 or higher
• 16.0 (modules amber-16)
  • variant amber-16-gpu activates all binaries, not only GPU version (even parallel and nonparallel versions, distinguished by suffixes .MPI, .cuda, .cuda.MPI). Usage of amber-16-gpu is preferred due to better optimization.
• 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)
  • variant amber-14-gpu8 activates all binaries, not only GPU version (even parallel and nonparallel versions, distinguished by suffixes .MPI, .cuda, .cuda.MPI). Usage of amber-14-gpu8 is preferred due to better optimization.
• 8, 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 amber-12-shmem)
      • modules available: amber10, amber10-parallel, amber-12, amber-12-pgi, amber-12-shmem, amber8.

Example

$ qsub -l select=2:ncpus=4:mem=10gb:scratch_local=4gb job.sh

where job.sh follows

#!/bin/sh
#
# name of the job
#PBS -N job
#
# messaging of end of the 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

Documentation

http://ambermd.org

Homepage

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