ADL: regarding active site

Oleg Trott trott at scripps.edu
Tue Jun 16 04:45:26 PDT 2009


David,

What problem are you referring to? If it's ligands going far outside
the search space then, like I just wrote, I don't think it will happen
in Vina.

Oleg

On Sun, Jun 14, 2009 at 1:30 PM, Davide
Mercadante<dmer018 at aucklanduni.ac.nz> wrote:
> Dear Oleg,
>
> sorry for the late reply. I am using Autodock 4 and not Autodock Vina. So,
> do you advice me to use Vina?
>  Do you think I will be able to solve the problem?
>
> Cheers,
> Davide
>
> 2009/6/14 Oleg Trott <trott at scripps.edu>
>
>> On Fri, Jun 12, 2009 at 3:53 PM, Davide
>> Mercadante<dmer018 at aucklanduni.ac.nz> wrote:
>>
>> > 2) After the calculations the docked ligands are not in the box that I
>> built
>> > to perform the calculation
>>
>> Are you using AutoDock 4 or AutoDock Vina? In Vina, there is a stiff
>> scoring function penalty for going outside the box, so the ligand is
>> very unlikely to stray too far.
>>
>> Oleg
>> --
>> Oleg Trott, Ph.D. (Columbia University)
>>
>> http://olegtrott.com
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-- 
Oleg Trott, Ph.D. (Columbia University)

http://olegtrott.com



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