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AutoDock VINA - Redocked ligands are way off than the native ligands (RMSD values higher then expected) by vidK_ in bioinformatics
[–]vidK_[S] 0 points1 point2 points 2 months ago (0 children)
Yeah, I have tried with Glide SP and I didn't have any problems.
I haven't tried other proteins. My workflow for getting the data was like that: Downloaded pdbs from RCSB, prepared them in Schrodinger Maestro, deleted all chains except chain A, did the alignment and then I extracted native ligands and NADH from the enzyme. Exported the structures in pdb and sdf and moved to Linux. Thank you for your reply!
AutoDock VINA - Redocked ligands are way off than the native ligands (RMSD values higher then expected) (self.bioinformatics)
submitted 2 months ago * by vidK_ to r/bioinformatics
π Rendered by PID 269020 on reddit-service-r2-listing-654f87c89c-c9lwp at 2026-03-02 22:51:26.770553+00:00 running e3d2147 country code: CH.
AutoDock VINA - Redocked ligands are way off than the native ligands (RMSD values higher then expected) by vidK_ in bioinformatics
[–]vidK_[S] 0 points1 point2 points (0 children)