ADL: slow docking and dlg?

Kirk Beebe kbeebe at
Fri Apr 21 13:31:12 PDT 2006

Hi All,

I finally have gotten autodock installed (1.4.1 
complete2.4_binary_ppcDarwin8_acad_1.4.1) on a Mac G5 (OS X 10.4) and it is 
capable of launching without an error message.
I must still have something setup improperly as I am simply going through 
the "using autodock with autodocktools: a tutorial" with the same ligand 
and receptor files indicated therein and the job is taking an eternity.

Here are further details-----

In the "set search parameters.....genetic algorithm parameters" , I leave 
the default settings at 250,000 evals.  This job runs for several hours and 
finally finishes successfully.  Upon trying to retrieve the dlg file it 
takes several minutes and then error messages emerge.  In the python shell 
it states "memory error" and in my main shell it states (among other 
things) "can't allocate region". Although I am not an expert on 
interpreting the information derived from the top command, under CPUs it 
states 0% as the job runs.  Also the dlg file is over 500 mb.

As a quick test I knocked the evals way down to 2500 and it ran in a couple 
of minutes and I was able to retrieve and view the dpf file.

Are my expectations for my G5 off and is this the amount of computing power 
required for a single run?

I'd sure appreciate any info/advice that anyone may be able to provide.



         Kirk Beebe, Ph.D.
         The Skaggs Institute for Chemical Biology
         The Scripps Research Institute
         10550 North Torrey Pines Road
         Mail Code #BCC-379
         La Jolla, CA 92037
         Phone: (858) 784-8985
         Fax: (858) 784-8990

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