ADL: search space parameters in vina

yanyuna hiyanyuna at gmail.com
Tue Nov 26 06:25:37 PST 2013


On 2013年11月26日 21:39, Brian Moldover wrote:
> If the structure is liganded, center the box on the ligand and expand the
> search space to cover the ligand, plus maybe 2 angstroms on all sides to be
> safe. If the liganded structure is solved, and you know the interacting
> residues, you can draw the smallest box possible that captures those
> interacting residues, and the center can be determined by that box.
>
> It's a little trial and error, although Vina is not that sensitive to where
> you center the search space. What's important is to capture the binding site
> information.
>
> -Brian
>
> -----Original Message-----
> From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
> Behalf Of Jiza Formeca
> Sent: Monday, November 25, 2013 10:27 PM
> To: autodock at scripps.edu
> Subject: ADL: search space parameters in vina
>
> Hi
> Anyone has good advice for determining the search space parameters in vina?
> I need help with center_x, center_y, and center_z.
>
> Jiza
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Hi ,
Thank you for your reply. I want to search the whole protein to find all 
the possible binding sites. The small molecular is not a liganded ligand 
, but a small probe I construct myself . So I want to center the box on 
the protein . But I don't know how to save 2000 conformation ?


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