smina_HYDE
Smina Apr 2 2016. Based on AutoDock Vina 1.1.2. / SeeSAR 2016-12-08 / Open Babel 2.3.2
Ligand protonation : obabel -p7.4 + manual correction of N-oxide groups / Protein protonation : pdb2pqr --ff amber --ffout amber
3D conformations of ligand were generated using obabel. Ligands were protonated with obabel at pH 7.4. N-oxide groups were manually corrected since to attribute correct charge to O- and N+. Protein were protonated with pdb2pqr usinf amber force field parameters
smina was run with the following parameters : scoring = vinardo, num_modes = 60, exhaustiveness = 32; minimize_iters = 100
Poses were generated with smina. Pose were optimized with ProToss and HYDE as implemented in SeeSAR and scored with HYDE as implemented in SeeSAR. Poses ranked 1st with SeeSAR were selected. No visual inspection was used for pose selection.
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Yes