AMBER

Description

AMBER (Assisted Model Building with Energy Refinement) is the collective name for a suite of programs designed to carry out molecular mechanical force field simulations, particularly on biomolecules.  See Amber force fields,  AMBER consists of about 50 programs.  Two major ones are:

• sander: Simulated annealing with NMR-derived energy restraints
• pmemd: This is an extensively-modified version of sander, optimized for periodic, PME simulations, and for GB simulations. It is faster than sander and scales better on parallel machines.

How to Access AMBER

NERSC uses modules to manage access to software. To use the default version of AMBER, type:

% module load amber

To see where the amber executables reside (the bin directory) and what environment variables it defines, type

% module show amber

E.g., on carver,

% module show amber           (or type module show amber/10.0)
-------------------------------------------------------------------
/usr/common/usg/Modules/modulefiles/amber/10.0:

module-whatis	 Molecular dynamics simulations 
setenv		 AMBERHOME /usr/common/usg/amber/10.0 
setenv		 AMBER_DAT /usr/common/usg/amber/10.0/dat 
setenv		 OMP_NUM_THREADS 1 
prepend-path	 LD_LIBRARY_PATH /usr/common/usg/gcc/default/lib64 
prepend-path	 LD_LIBRARY_PATH /usr/common/usg/openmpi/default/gnu/lib 
prepend-path	 LD_LIBRARY_PATH /usr/common/usg/mkl/10.2.2.025/lib/em64t 
prepend-path	 PATH /usr/common/usg/amber/10.0/bin 

-------------------------------------------------------------------

To see the available executables, type

% ls -l /usr/common/usg/amber/10.0/bin

A user should choose an appropriate binary to run his/her jobs. The sander, sander.LES, sander.PIMD are the serial binaries, their prallel binaries are sander.MPI, sander.LES.mpi, sander.PIMD.MPI, respectively.

How to use AMBER on Hopper

There are two ways of running AMBER on Hopper: submitting a batch job, or running interactively in an interactive batch session. A sample batch script to run AMBER on Hopper:

#PBS -N test_amber
#PBS -q debug
#PBS -l mppwidth=48
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -V

cd $PBS_O_WORKDIR
module load amber

aprun -n 48 sander.MPI -i mytest.in -o mytest.out ... (more sander command line options)

Then submit the job script using qsub command, eg., assume the job script name is test_amber.pbs,

% qsub test_amber.pbs

To request an interactive batch session, issue a command such as this one (e.g., requesting 48 PEs):

% qsub -I -V -q interactive -l mppwidth=48 

when a new batch session is returned to you, type the following commands:

% cd $PBS_O_WORKDIR
% module load abmer
% aprun -n 48 sander.MPI -i mytest.in -o mytest.out ... (more sander command line options)

How to use  AMBER on Carver

A sample batch script for Carver:

#PBS -S /usr/bin/tcsh
#PBS -l nodes=1:ppn=8,walltime=0:30:00
#PBS -N test_amber 
#PBS -oe 
#PBS -q debug
#PBS -V

cd $PBS_O_WORKDIR

module load amber
mpirun -np 8 sander.MPI -i mytest.in -o mytest.out ... (more sander command line options)

Energy Minimization BPTI Example

Here we use AMBER to do an energy minimization of BPTI (bovine pancreatic trypsin inhibitor). This system, while rather small (536 atoms), is large enough to benefit from parallelism up to around 16 MPI tasks. Use is made of protonate and tleap to prepare the coordinates and topology for the simulation.

First execute the following script. The file 6pti.mod.pdb is an edited version of the file 6pti.pdb which is distributed by the Brookhaven Protein Data Bank. The water and phosphate have been deleted and the B conformations of residues 39 and 50 have been deleted.

module load amber

tleap
inside tleapi, type

source leaprc.ff03
bpti = loadPdb 6pti.mod.pdb
bond bpti.5.SG bpti.55.SG
bond bpti.14.SG bpti.38.SG
bond bpti.30.SG bpti.51.SG
saveAmberParm bpti prmtop prmcrd
quit

#this generates "prmcrd" and "prmtop" files

# run sander

cat << eof > min.in
# 200 steps of minimization, generalized Born solvent model
 &cntrl
    maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
 &end
/
eof

Documentation

Amber Home Page

Availibility