vina_HYDE
vina 1.1.2 (may11, 2011) / 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
Vina was run with default parameters, 20 poses were generated
Poses were generated with vina. 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.
No
Yes