ADL: BLIND DOCKING_grid problem

Garrett M. Morris garrett at scripps.edu
Thu Mar 6 16:53:24 PST 2008


Dear Richa,

On 6 Mar, 2008, at 1:07 am, zhaojunwei wrote:

> Hi, Richa
> I think you can change the grid points in your .gpf file directly.
>
> receptor *.pdbqs                     # macromolecule
> gridfld *.maps.fld                   # grid_data_file
> npts 100 100 100                     # num.grid points in xyz
> spacing 0.375                        # spacing(A)
>
> Hope it helps.
>
>
>
>
> 在2008-03-06,"Richa Batra" <richa.batra at gmail.com> 写道:
>
> Dear all,
> I am trying blind docking. When i visualize the grid it covers my  
> whole
> protein. According to the calculations if i set 100 points in each  
> axis it
> should be covering my entire protein.However in .glg file what i  
> find is a
> smaller grid is formed everytime. Please help me.
>

Did you try increasing the spacing from the default value (0.375  
Angstroms)?

> -- 
> Regards
> Ms Richa Batra
> Bioinformatics Centre,
> Universtiy of Pune,
> Pune, MHT, India.
> Alt. Id: batra.richa at yahoo.com
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___
Dr Garrett M. Morris, M.A. (Oxon.), D.Phil. (Oxon.)

The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
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