GOLD/AUTODOCK VINA
GOLD/AUTODOCK VINA/SCHRODINGER
(prepwizard) -propka_pH 7.5 (prepwizard) -fillsidechains -s (ligprep) -adjust_itc -ph 7.0
Maestro's prepwizard was used to optimize the protein with pH value and fillsidechains option. Maestro's ligprep was used to generate optimized 3d structure of ligands from 2d structure.
autoscale = 1.5; floodfill_center = cavity_from_ligand 10 atoms; gold_fitfunc_path = plp # use ChemPLP as scoring function to generate poses; num_poses = 200 # generate 200 poses as pose_pool for each complex
PHE211 and PHE70 are set as flexible. AutoDock Vina is used to rescore the poses.
No
No