[Dock-fans] System resouces for virtual screening
jji at cgl.ucsf.edu
Thu Oct 20 13:19:17 PDT 2005
I am learning to use DOCK in virtual screening, still not succeeded with
the Sphere generator yet, but I am wondering if a Labtop, pentium 4, win XP
(Dell) could handle this job? If yet howlong it will take? I read Irwin's
paper on Biochemistry and see them running in days to a week on a
[JJI] You can definitely dock on a single P4 machine. Having more machines
will give you results faster, of course. There is a speed difference between
DOCK5.2 and the version of DOCK used in the Biochemistry paper (Irwin,
Raushel, Shoichet 2005) which was DOCK3.5.54.
If I have only the above mention system, is it possible for me to run
virtual screening? even with just a subset of the ZINC or NCI database?
Thank you for your time
By the way, I applied all the patches and still got Segmentation Fault when
I run SPHGEN with the demo rec.ms, I would appreciate if someone here could
give me some suggestions.
(I have reduced the surface file of my own to less than 1/4 of the size of
rec.ms but still fail)
Le Tien Dung, PhD
The Microbial Function Laboratory
National Food Research Institute (NFRI)
Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642 - JAPAN
E-mail: ledt at affrc.go.jp
URLs: http://www.nfri.affrc.go.jp <http://www.nfri.affrc.go.jp/> &
om/unlimited/> Music Unlimited - Access over 1 million songs. Try it free.
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