Stuck at 0% Vina
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Hello,
I'm struggling running autodock vina with proteins, even with huge PC specs, I'm stuck at 0% while using Wine to run the windows version.
Any help would be welcome, thanks
Hello, sorry, I don't know why it is stuck at 0%. If you can uploaded input pdbqt files here, I can try it with the latest version without Wine to see if it works.
I ran in on multiple computers, one struggled a week to dock a peptide on a protein, and I though the debian server would run way more quickly, but it's just a lack of patience.
As I talk to you, I have a question about exhaustiveness. My 56 thread CPU isn't used fully with 8 exhaustiveness. The 8 accuracy is fine for me, do increasing exhaustiveness will provide better results for running Vina?
Thanks
Good question. Increasing exhaustiveness will provide better results, however since it is already struggling to dock a peptide, it would take much longer to run. Perhaps it would be better to limit the number of active torsion on the peptide. You can limit the number of active torsions before making pdbqt files using Edit > Preferences > AutoDock > Ligand Preparation > Number of torsion: option.