[Chimera-users] inquire about molecular docking

[Elaine Meng]

Hi Mohamed,
It is expected (not a problem but normal) that changing the input may change the output.  You have to decide which is the better input to use.   

As I said in the previous message, however, it may be more important to use a different docking tool, not the one in Chimera.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jul 31, 2019, at 1:00 AM, Mohamed Hegazy <mohamedhegazy219427 at gmail.com> wrote:
> 
> 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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