ADL: RE: Grid Box

SRMD, Col - Platt, Steven Steven.Platt at hpa.org.uk
Fri Sep 10 05:21:17 PDT 2004


Aurora,

The easiest way to manipulate the grid box is to use AutoDock Tools (ADT).
The graphical interface allows you to place and resize your grid box
accurately and interactively. You can also adjust the relevant parameters in
the .gpf file (as Gyanendra mentioned). If the maximum dimensions
(126x126x126) do not cover your area of interest, try increasing the spacing
between points in the grid. The default spacing of 0.375 angstroms can be
increased up to a maximum of 1 angstrom, but you need to remember that
larger point spacing will reduce the resolution of your dockings. Also,
larger grids will obviously take longer to compute.
I use autodock 3.0.5 and have used these values above.

I hope this helps.

Steve

Steve Platt
Bioinformatics Support Co-ordinator
Genomics, Proteomics & Bioinformatics Unit
HPA Colindale
61 Colindale Avenue
London
UK

-----Original Message-----
From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
Behalf Of Costache, Aurora
Sent: 09 September 2004 22:43
To: autodock at scripps.edu
Subject: ADL: Grid Box

Hello all,
 
I would like to ask if anybody know how I can increase the grid box for a
docking calculation. Which file I have to modify?
Thank you very much,
Aurora
 
Aurora Costache
Graduate Student
Department of Chemistry 
Marquette University 
535 N 14th Street 
PO Box 1881 
Milwaukee, WI 53201 

phone: 414-288-2081/5291 
email: aurora.costache at marquette.edu 

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