[Chimera-users] inquire about molecular docking

[Elaine Meng]

To explain in more detail: 

I understand you would like to get the same (or almost same) result from the two starting structures, since they are really the same ligand molecule.  

However, to try to converge multiple calculations with different starting structures to the same or similar result, you would need to do much longer, more intensive docking calculations.  Longer calculations are needed for sampling many more positions and conformations of ligand and receptor.  This Chimera tool does not allow long docking calculations.

I hope this  is clear now. Best,
Elaine


> On Jul 31, 2019, at 8:08 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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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