[Chimera-users] Hydrogen Bond numbers

[Elaine Meng]

Hi Dustin,
There may be some stochasticity in the Vina sampling (e.g. use of random number generator), but I don’t know for certain. We are not the Vina developers, you may want to delve into their documention and publications. AutoDock Vina website:
<http://vina.scripps.edu/>

Of course, if the output positions are slightly different, it makes sense that the numbers of H-bonds are different.

HOWEVER… your dialog shows that the ligand and the receptor are the same model.  This makes no sense.  I assume you aren’t really trying to dock a protein to itself.  There are other indicators of this crazy situation, like the results saying that the ligand has 1070 active torsions (rotatable bonds).

As I understand it, Vina is mainly for docking small molecules to proteins.  Even if you wanted to try to use it for protein-protein docking, the amount of sampling available through this web service is quite small and unsuited to the task.  If you really did want to do protein-protein docking, you may want to look into other available tools.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 11, 2018, at 1:54 PM, Dustin Park <dpark61 at illinois.edu> wrote:
> 
> Hello,
> 
> Sorry, I had inserted the wrong second image. I attached another image. 
> 
> <image.png>
> 
> 
> On Wed, Apr 11, 2018 at 3:32 PM, Dustin Park <dpark61 at illinois.edu> wrote:
> Hello,
> 
> After using autodock and obtaining the HBonds, it seems that if I run the simulation with the exact same parameters for receptor search volume, the HBonds numbers change along with some other information. I have added the file images to show. Is this supposed to be happening or is this a user error?
> 
> 
> <image.png>
> First run:
> <image.png>
> Second Run with same parameters:
> <image.png>
> 
> 
> Thank you!