ADL: autodock Digest, Vol 98, Issue 5

Dinler Antunes dinler at gmail.com
Fri Oct 12 04:29:54 PDT 2012


Hi S., thanks for the tips.

I have performed some tests and the Binding Energies are really better if I
narrow down the Grid Box to the place I know the ligand must be, inside the
cleft, but this also limits the space of search for better side chain
conformations. I don't actually now what the program will do performing
local optimization only. The results would be equivalent as having the
normal docking but without the translation and rotational search? Just
conformational search for the rotatable bonds?

-- 
Dinler Amaral Antunes

------------------------------
>
> Message: 6
> Date: Thu, 11 Oct 2012 11:57:14 -0700
> From: Stefano Forli <forli at scripps.edu>
> Subject: Re: ADL: Using input coordinates as a seed
> To: <autodock at scripps.edu>
> Message-ID: <5077168A.2010505 at scripps.edu>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> 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.
>
>      tel: (858) 784-2055
>      fax: (858) 784-2860
>      email: forli at scripps.edu
>      http://www.scripps.edu/~forli/
>
>
> ------------------------------
>
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> End of autodock Digest, Vol 98, Issue 5
> ***************************************
>



-- 
Dinler Amaral Antunes


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