ADL: Using input coordinates as a seed

Stefano Forli forli at scripps.edu
Thu Oct 11 11:57:14 PDT 2012


Hi,

if what you want is to minimize your structure in the active site, you could force the 
docking to be limited to the current ligand position (i.e. setting the grid box to the 
minimal size to contain the ligand) or perform a local search only (see 'vina 
--help_advanced').

Hope this helps,

S.

On 10/11/2012 04:46 AM, Dinler Antunes wrote:
> Hi,
>
> I'm a Brazilian PhD student I want to know is if there is how to make
> Autodock Vina use as a seed the position in which the input
> ("ligand.pdbqt") is provided. Instead of using a random seed. I'm working
> on a special case of protein-ligand docking in which I know the right
> position of the ligand backbone (peptide), and I just want to adjust the
> ligand side-chains using Vina. But using random seed the program is not
> finding the way to the best position inside the binding site (gets stuck in
> a local minima, even using bigger exhaustiveness).
>
> Thank you very much for your attention,
>

-- 
  Stefano Forli, PhD

  Staff Scientist
  Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-112
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

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     email: forli at scripps.edu
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