[Dock-fans] anchor orientation

Dariusz Ekonomiuk ekodarek at icm.edu.pl
Tue Apr 27 10:26:08 PDT 2010


Thank you Trent
"Fix Anchor Docking" is what I was looking for.

best,
  Dariusz

>
>
>  Hi Dariusz,
>
> You can turn off ligand orientation by the following:
>
>   orient_ligand    no
>   flexible_ligand  yes
>
> This will grow out your ligands starting from the anchor in your beginning
> orientation.
> In the Rizzo group, we call this procedure Fix Anchor Docking.
>
>
> Note that the anchor will still move because of the simplex minimizer.
>
> I hope this helps,
>
>
>
> Trent E. Balius
> Graduate Student, Rizzo Group,
> Department of Applied Mathematics and Statistics,
> Stony Brook University.
> Office: Math Tower 3-129, Phone: (631) 632-8519
> URL: http://www.ams.sunysb.edu/~tbalius/
>
>
>
>
>
> -----Original Message-----
> From: Dariusz Ekonomiuk <ekodarek at icm.edu.pl>
> To: dock-fans at mailman.docking.org
> Sent: Tue, Apr 27, 2010 5:10 am
> Subject: [Dock-fans] anchor orientation
>
>
> Dear all,
>
> I have a question related to anchor and grow algorithm as implemented in
> DOCK 6.3.
> Would it be possible to use user defined orientation of the anchor ?
> In other words, I would like to start with predefined coordinates of the
> anchor and then use DOCK
> for growing the layers.
> I assume it would require modifications in the source code,
> any hints ?
>
> best,
> Dariusz Ekonomiuk
>
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>
>




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