ADL: slow docking and dlg?
kbeebe at scripps.edu
Fri Apr 21 13:31:12 PDT 2006
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
More information about the autodock