CADD course learning (7) -- Simulation of target and small molecule interaction (flexible docking autodock)

CADD Course study （7）-- Simulate the interaction between the target and small molecules （ Flexible docking AutoDock）

Semi flexible docking VS Flexible docking

Semi flexible

1. A utodockTools ligand 、 Receptor document preparation ：
   ① Delete water and add H atom 、 Charge 、 Combine nonpolar hydrogen 、 Set the ligand rotatable key ;
   ② preservation lig.pdbqt and rec.pdbqt;
2. AutoGrid Grid calculation ：
   ① choice rec.pdbqt, Set the probe atom type , Set the size and position of the box ;
   ② preservation dock.gpf function AutoGrid Program calculation grid , Output dock.glg;
3. AutoDock Docking calculation ：
   ① choice lig.pdbqt and rec.pdbqt, Set up conformation search ;
   ② preservation dock.dpf, function AutoDock Program calculation grid , Output dock.dlg;
   flexible
4. Autodock Tools ligand 、 Receptor document preparation ：
   ① Delete water and add H atom 、 Charge 、 Combine nonpolar hydrogen 、 Set the ligand rotatable key ;
   ② preservation lig.pdbqt、rec rigid.pdbqt and rec_flex.pdbqt;
5. AutoGrid Grid calculation ：
   ① choice rec_rigid.pdbqt, Set the probe atom type , Set the size and position of the box ;
   ② preservation dock.gpf, function AutoGrid Program calculation grid , Output dock.glg; work
6. AutoDock Docking calculation ：
   ① choice lig.pdbqt、rec rigid.pdbqt and rec_flex.pdbqt Set the receptor flexible residue rotatable key , Set up conformation search ;
   ② preservation dock.dpf, function AutoDock Program calculation grid , Output dock.dlg

Generate lattice ：.\autogrid4.exe -p .\dockflex.gpf

Command line ： .\autodock4.exe -p .\dockflex.dpf