How to Run AMBER

AMBER, that stands for Assisted Model Building with Energy Refinement, is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules.

Version 10 of AMBER has been installed on Lewis.

On lewis, it is installed under /share/apps/amber10.  The executables are under /share/apps/amber10/exe.

1. Set the PATH Environment Variable

Users may include the executables in their PATH by typing the following command so that they don’t have to include the path in their commands to run the AMBER program/tools.

export PATH=$PATH:/share/apps/amber10/exe

or add the above command to your “~/.bashrc” file.

2. Prepare Input Files

Before running AMBER, users must generate AMBER topology and coordinate files. The following are a simple example to run an AMBER(GB) minimization for “test.pdb”.

First, create a script file named “test.leap.scrpt” that includes the following line:

source leaprc.ff03
set default PBradii bondi
mol = loadpdb test.pdb
saveamberparm mol test.prmtop test.prmcrd
quit

where “leaprc.ff03″ is the AMBER force field parameter file.

Then, run “tleap” by typing on command line:

tleap -f test.leap.scrpt

This will generate the topology file “test.prmtop” and coordinate file “test.prmcrd”.

3. Run AMBER Jobs

There are both serial and parallel versions of the executables.  

1) Run Serial Jobs on Lewis

The serial version can be run with the following command

bsub -J jobname -oo jobname.o%J -eo jobname.e%J sander -O -i inputfile -o outfile -p test.prmtop -c test.prmcrd -r test.restrt

where the input file “inputfile” looks like this

Minimization
&cntrl
imin=1, maxcyc=100,
cut=300.0, igb=2, saltcon=0.2, gbsa=1,
ntpr=10, ntx=1, ntb=0,
&end

2) Run Parallel Jobs on Lewis

The parallel versions have a qualifier of “.MPI” on the end, e.g. sander.MPI.  A sample LSF job script on lewis, for the parallel version of sander might look like:

# Set job parameters
#BSUB -a openmpi
#BSUB -J jobname
#BSUB -oo jobname.o%J
#BSUB -eo jobname.e%J

# Set number of CPUs
#BSUB -n 4

# Start AMBER job
mpirun.lsf sander.MPI -O -i inputfile -o outputfile -p test.prmtop -c test.prmcrd -r test.restrt

4. Convert the Minimized Coordinates to a PDB File

The miminized structure can be converted to the PDB file by the following command

ambpdb -p test.prmtop < test.restrt > test_min.pdb

*There are a number of tutorials prepared by the AMBER developers about learning how to use the AMBER software suite, which are listed as follows.

•  Some general AMBER tutorials for both basic and advanced users
• A tutorial for the AMBER’s general Born (GB) model
• Another tutorial for the AMBER’s general Born (GB) model

For more information of AMBER, see the Amber Users’ Manual.