ADL: BLIND DOCKING_grid problem

snoze pa snoze.pa at gmail.com
Wed Mar 12 14:02:51 PDT 2008


Do the simple Math here..

 You grid size is 100x100x100 and spacing is 0.375

So the size of the box(one side) is : 100x.375=37.5A

Check what is your protein size? also it is important to select the grid
center in autodock.
Make sure your grid center is right one. If you think that the gridcenter is
right then you can edit the .gpf file and modify the grid size to smaller
value.

hope this will be helpful.




2008/3/6 zhaojunwei <zhaojunwei2004 at 126.com>:

> 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.
>
> --
> Regards
> Ms Richa Batra
> Bioinformatics Centre,
> Universtiy of Pune,
> Pune, MHT, India.
> Alt. Id: batra.richa at yahoo.com
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