AutoDock Vina
AutoDock Vina 1.1.2
Autodock Vina restraints
Assumed pH 7.4
We assigned protonation states and initial ligand conformations with MarvinSketch and the MMFF94 force field (100 conformers, 0.1 diversity limit). Ligands were geometry optimized in Gaussian with the AM1 semi-empirical method (VSTO-3G), followed by file preparation in Autodock Tools. The given Apo protein was protonated in Chimera, followed by preparation in Autodock Tools. Docking was conducted with Autodock Vina.
Bevan Lab Ranking Protocol (na
MarvinSketch 16.10.31, Gaussian 09, Autodock Tools4), Autodock Vina 1.1.2, UCSF Chimera
MMFF94 followed by AM1 geometry, Autodock Tools ligand charges, Chimera histidine protein charges
We assigned protonation states and initial ligand conformations with MarvinSketch and the MMFF94 force field (100 conformers, 0.1 diversity limit). Ligands were geometry optimized in Gaussian with the AM1 semi-empirical method (VSTO-3G), followed by file preparation in Autodock Tools. The given Apo protein was protonated in Chimera, followed by preparation in Autodock Tools. Docking was conducted with Autodock Vina.
Autodock Vina restraints
Autodock Vina 1.1.2