[Chimera-users] Autodock vine problem

[Robin]

Hello,
In this context I want to that why the result of docking gives mangled
ligand?
I used web service mentioned in the last paragraph of Elaine's reply to
Tunc.
The poses listed in viewdock when observed in chimera main display, I found
the ligand was not in its original structure.
improper Bonds in ligand were added and its structure was mangled!
What is the reason for this?

 -Robin Parmar
PhD Research Scholar
Dept of Zoology,
Gujarat University
India.

On 1 April 2015 at 23:26, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Tunc,
> We do not have any control over your local installation, or whether you
> even have it installed locally! It is not included with Chimera. If you
> didn’t install it yourself, you should check with whoever did install it.
>
> However, I could use the AutoDock Vina web service at NBCR successfully -
> I ran it just now in Chimera version 1.10.1 with the default server setting
> for the “Opal web service” option under Executable location.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Apr 1, 2015, at 9:02 AM, Tunc Morova <morovatunc at gmail.com> wrote:
>
> > Hello,
> >
> > I was trying to use built-in auto dock vina tool of chimera. I came a
> cross with an error saying
> >
> > service local`c:\”program filex(x86)”\”the scripps research
> Institute\Vina\Vina.exe` is unavailable.
> >
> > I have been checking forums for a longtime. Unfortunately, i couldn’t
> run the docking. couple days ago, I think i accidentally ran the docking
> locally but i am not sure.
> >
> > Is my pathing correct? how can my local auto dock vina be unavaible ?
> >
> > Please help me for finishing my thesis :D
> >
> > Thank you for your support
> >
> > -Tunc
>
>
> _______________________________________________
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> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
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