[Dock-fans] System resouces for virtual screening

John Irwin jji at cgl.ucsf.edu
Thu Oct 20 13:19:17 PDT 2005


Hi Le
 
 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
workstation. 
[JJI]  
[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. 
 
Good luck!
 
John
 

 

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

 

Le

 

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/>  &
http://www.cynosura.org (personal)


 



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