ADL: Fwd: PBS script for virtual screening

Garrett M. Morris garrett at
Sun Jan 20 18:34:36 PST 2008

Dear Amor,

Begin forwarded message:

> From: "Amor A. San Juan" <amorasj at>
> Date: January 18, 2008 1:31:52 am PST
> To: autodock at
> Subject: ADL: PBS script for virtual screening
> Reply-To: autodock at
> Hi everyone,
> I need help in writing a PBS script to submit to linux cluster. I  
> am stuck
> and need your assistance so greatly, as I dont have enough programming
> skills.

I am attaching a copy of a Python script that we use to submit  
AutoDock jobs to our cluster, using its PBS queueing system:

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This assumes that the path to autodock4 is "/applications/autodock".   
You will need to edit this to point to where your AutoDock binary  
installation is.

This script will require Python to be installed, which is included on  
most Linux and Mac OS X platforms.

I hope this helps,


> 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
> cluster.
> Below is the default PBS script, which I dont have precise idea on  
> how to
> put some arguments prior submitting to cluster.
> #!/bin/sh
> #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 -V
> #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  
> script
> submitted to cluster?
> Thanks
> Amor
> ________________________________________________
> --- ADL: AutoDock List  --- 
> mailing_list ---

Dr Garrett M. Morris, MA, DPhil

The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: garrett at
La Jolla,  CA 92037-1000,  USA.

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