[Chimera-users] inquire about molecular docking

Mohamed Hegazy mohamedhegazy219427 at gmail.com
Wed Jul 31 01:00:30 PDT 2019

Thank you for the information! But I think you don't understand what I mean
my problem is that in ligand preparation the initial structure of ligand
differs from the minimized one .. and that affects the docking result ..

Mohamed Said Hegazy

On Tue, Jul 30, 2019, 10:51 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Mohamed Hegazy,
> Autodock Vina is a separate program (not inside Chimera) and you should
> check its website for more information about how it works:
> <http://vina.scripps.edu/>
> The Chimera tool named “Autodock Vina” just connects to an outside web
> service that is running Autodock Vina.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> This web service is a shared resource and does not allow very much
> sampling of space, and it only allows docking one small molecule at a time.
> Therefore, as mentioned in the help page linked above, we do not recommend
> using it for most research purposes.
> If you want to do better (more intensive) sampling of space, and/or dock a
> lot of small molecules to compare to each other, you should download
> Autodock Vina from the website above and run Autodock Vina directly.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jul 30, 2019, at 10:50 AM, Mohamed Hegazy <
> mohamedhegazy219427 at gmail.com> wrote:
> >
> > Hey ,
> >           My name is Mohamed Hegazy, beginner in molecular docking  ,
> recently I performed a molecular docking procedure using chimera and  I
> found that the initial structure of the ligand differs from the minimized
> one , and the binding score for a ligand would change during my different
> runs. The binding score you obtain from my docking cannot be a constant
> number.
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