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@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.