I am thankful and grateful to everyone for guiding me through.
Regards,
Thripthi S.
On Mon, Nov 20, 2023 at 1:50 PM Subhomoi Borkotoky
wrote:
> Hi,
>
> Probably you are not setting the grid right. Try the AMDock tool, it uses
> Autodock vina. Here you can specify your residues, and the grid
Hi,
Probably you are not setting the grid right. Try the AMDock tool, it uses
Autodock vina. Here you can specify your residues, and the grid will be
prepared accordingly.
https://github.com/Valdes-Tresanco-MS/AMDock-win
Thanks & Regards,
--
*Subhomoi Borkotoky, Ph.
It is most likely the spacing setting in PMV (it is set to the default
value used by the original Autodock, namely 0.375A). In Autodock Vina it
should be set to 1 angstrom.
Let me know if this helps
Kind regards,
Sorin
On Sun, Nov 19, 2023 at 1:57 PM BRUNO DI GERONIMO QUINTERO <
Hello Thripthi S. ,
Given the information you provide, it is quite difficult to figure out what
your issue is with VINA. If you provide me the data (receptor, ligand, and
box), I can do some tests, to see what's happening. In VINA, *pdbqt files
for both receptor/ligand are the most tricky part to
Greetings to all,
I have performed docking through Glide and Autodock vina for a protein
for which the active site has been taken from the literature. Glide is able
to dock the compounds correctly in the active site whereas autodock vina
does not dock the compounds within the specified site. I
