ADL: PBS script for virtual screening

Wilfred Li wilfred at
Fri Jan 18 08:40:43 PST 2008

The Scripps virtual screening tutorial contains a PBS sample script for
use on their bluefish cluster, which is also available at the NBCR
Summer Institute archive, The
last two pages.

It's best to discuss with your cluster administrator as well since they
are normally able to provide a version that works with the local



-----Original Message-----
From: autodock-bounces at [mailto:autodock-bounces at]
On Behalf Of Amor A. San Juan
Sent: Friday, January 18, 2008 1:32 AM
To: autodock at
Subject: ADL: PBS script for virtual screening

Hi everyone,

I need help in writing a PBS script to submit to linux cluster. I am
and need your assistance so greatly, as I dont have enough programming

I already generated all the rest of input files for executable autodock,
such as *dpf, gridmaps etc. Now I need simple PBS script to submit to

Below is the default PBS script, which I dont have precise idea on how
put some arguments prior submitting to cluster.

#PBS -l arch=x86_64
#PBS -q MP
#PBS -l nodes=4:ppn=4:smp
#PBS -l ncpus=4
#PBS -l walltime=00:05:00
#PBS -l mem=100mb
#PBS -m bea
#PBS -o Output_File
#PBS -e Error_File
mpirun -np 4 -machinefile $PBS_NODEFILE ./a.out

Would someone please explain in detail or send a file of  the  PBS
submitted to cluster?


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