ADL: Making a cluster to perform docking

Wilfred Li wilfred at
Thu Jan 31 11:09:40 PST 2008

Why not use Rocks?



-----Original Message-----
From: autodock-bounces at [mailto:autodock-bounces at]
On Behalf Of kala
Sent: Sunday, January 27, 2008 8:34 PM
To: autodock at; Daniel Jana
Subject: ADL: Making a cluster to perform docking

                  I wish i coluld seek a little advice in building a
computer to perform multiple docking experiments using Autodock
The Bioinfo Dept in our university has arranged new computers and the
configuration goes

66- core 2 duo @ 2.4 Ghz, each one with 2 Gb RAM and 160 Gb hard drive ,
10/100 Ethernet and all are currently configured with windows XP.
they have asked for a proposal from students for designs to make a
out of them and can be used for performing multiple dockings at a time
for parallely implemeting the autodock and also for molecular dynamics

Can you please help me in designing a cluster out of them,
they all can be loaded with linux.I know how to access all the computers
>From a single computer by SSH and evoke the AD from each computer, but
feel this is a crazy idea to perform it , Can you guys suggest me a
idea and how in your place people use AD and how i can automate the
and also Is parallel AD possible?

you can also personally mail me at kalabharath at

with regards

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