ADL: search space parameters in vina

yanyuna hiyanyuna at
Tue Nov 26 06:28:32 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 [mailto:autodock-bounces at] On
> Behalf Of Jiza Formeca
> Sent: Monday, November 25, 2013 10:27 PM
> To: autodock at
> 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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I want to know if the result of the Autodock Vina has been clustered or 
just several conformations?

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