[Dock-fans] max spheres limit

[Ben Keshet]

Dear all,

Sudipto recently commented about the limitation of the max number of spheres
being 50-75.  I have found a similar comment about dock5.3:
http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2005-December/000508
.html

Can anyone support or provide any more information about the limitation of
Dock with large clusters? Is Dock6.1 any better than 5.3 with regard to
that? Is the limit different for rigid and flexible docking? Is there any
intelligent way to overcome that limit?  

75 spheres are often too small for my ligands.  I could manually edit the
SPH file and delete less likely spheres, but I would prefer avoiding such
speculations.  

Any comments are greatly appreciated,

Ben



Date: Fri, 28 Dec 2007 23:17:50 -0800 (PST)
From: Sudipto Mukherjee <sudmukh at yahoo.com>
Subject: Re: [Dock-fans] bad allocation
To: DOCK Fans Mailing List <Dock-fans at docking.org>
Message-ID: <834289.7216.qm at web36707.mail.mud.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

Dear Barbara,

Docking works well with about 50-75
spheres in the binding site. Could you specify how many spheres you are
using? Are all roughly in the binding site? Selecting more spheres
would increase the box size for the grid. The size the grid file
increases roughly as the cube of the box size i.e. proportional to the
volume of the box.

I have tested DOCK successfully with grid
files as large as 800MB on a computer with 2GB RAM . However, if the
grid file is larger than the amount of available memory, memory
allocation errors like the one described is likely.
 
Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
Lab: 631-632-8519, Mobile: 631-220-5744