Running Amber 9.0 on the Xeon Linux Cluster

 

Amber consists of around 60 programs.  Each can be run interactively or as a batch job.  Please note that the interactive limit is 30 minutes. More information on Amber program can be found in the Amber web page.

 

Interactively

 

We will use an example for setting up duplex DNA: polyA-polyT from on-line tutorial:

 

1.  Copy the nuc.in file from the AMBER directory into your working directory:

 

tunb:% cp /usr/apps/chemistry/AMBER/intel9/amber8/amber/tutorial/polyA-polyT/nuc.in nuc.in

 

2.  Set the AMBERHOME environment variable and the executables:

 

tunb:% setenv AMBERHOME /usr/apps/chemistry/AMBER/Amber9/amber9

tunb:% set path = ( $path $AMBERHOME/exe )

 

3.  Run nucgen:

 

tunb:% nucgen -O -i nuc.in -o nuc.out -d $AMBERHOME/dat/leap/parm/nucgen.dat -p nuc.pdb

 

4. Run xleap:

 

tunb:% xleap -f leaprc.ff94

 

 

 

 

 

As a batch job

 

To run Amber 7.0 as a batch job, first you need to create a batch script.  This link provides more information about running jobs on the Xeon Linux Cluster.  After creating the script, you can then submit your job to the batch system using the following command:

 

         tunb:% bsub < batch_script_name
 
Using the example from the same on-line tutorial:
 
1.             Copy the necessary files into your working directory:
 
tunb:% cp /usr/apps/chemistry/AMBER/intel9/amber8/tutorial/polyA-polyT/fixit.in fixit.in
tunb:% cp /usr/apps/chemistry/AMBER/intel9/amber8/tutorial/polyA-polyT/polyAT_vac.inpcrd polyAT_vac.inpcrd
tunb:% cp /usr/apps/chemistry/AMBER/intel9/amber8/tutorial/polyA-polyT/polyAT_vac.prmtop polyAT_vac.prmtop
 
       2.  Create a batch script file:
The following is an example of batch script file for running sander (please change the variables based on your needs):

 

#!/bin/csh

#BSUB -n  4                                # Specify 4 processes

#BSUB -W 1:00                          # Specify job run time limit of 1 hour

#BSUB -o amberjob.%J.o           # Store the standard output and standard error of the

                                                    # job in file testjob.jobid.o (optional)

#BSUB -J amberjob                    # Specify job name (optional)

 

setenv AMBERHOME /usr/apps/chemistry/AMBER/Amber9/amber9

set path = ( $path $AMBERHOME/exe )

 

cmpirun -np 4 -lsf sander.MPI -O -i fixit.in -o fixit.out -c polyAT_vac.inpcrd -p polyAT_vac.prmtop  -r fixit.restrt -ref polyAT_vac.inpcrd

 

  1. Submit the job to the batch system:

 

tunb:% bsub < batch_script_name