AUTODOCK 4.

: e-mail: jolin31912811@yahoo.com.tw
AutoDock docking (receptor)
autodock4 .0

PS.

*AUTODOCK4.0

()
1. File -> Read Molecule ()
2. Select -> Select From String() -> Add
3. Edit -> Delete -> Delete AtomSet -> Continue()
4. Edit -> Hydrogen -> Add -> OK
5.File -> Save -> Wrtie PDB
6. Display -> Show/Hide Molecule ( ligand)

()/* Ligand */
1.Ligand -> input -> open -> (.pdb)
2.Ligand -> Output -> Save as pdbqt

() autodock4.0 (Flexible Residues)

A
File -> Save -> Write PDBQT
B
1.Flexible Residues -> Input -> Choose Macromolecule
2.Edit -> Hydrogens -> Merge Non-Polar -> CONTINUE
3.Select -> Select From String /* Residue ARG8 -> Add */
4.Flexible Residues -> Choose Torsions in Currently Select Resdues
5.Flexible Residues -> Oput -> Save Rigid pdbqt

() /* Grid */
1.Grid -> macromolecule -> (.pdbqt) (protein)
2.Grid -> Set Map Type -> (.pdbqt) (ligand)
3. Grid -> Grid Box () ->
4. File(Grid Options) -> Close saving current
5. Grid -> Output -> Save GPF (.gpf)
6. /* Edit GPF (.gpf) */

() /* Run */
1.Run -> Run AutoGrid
2.Laumch (autodcok3 autodcok4 )
PS.

() /* Docking */
1.Docking -> Mocromolecule -> (.pdbqt) (protein)
2.Docking -> Ligand -> (.pdbqt) (ligand)
3. Docking -> Output -> ()
4. /* Edit DPF (.dpf) */

() /* Run */
1.Run -> Run AutoDock
2.Laumch (autodcok3 autodcok4 )

() /* Analyze */
A
1.Analyze -> Docking -> (.dlg)
2.Analyze -> Conformations -> Play ( ligand ps.
)

3.Macromolecule -> (.pdbqt) (protein)

() /* Analyze */
B
1. Analyze -> Grids -> Open Other [() autogrid

]
2.Analyze -> Conformations -> Play (ligand autodock

docking )

() /* Analyze */
C
1. Analyze -> Conformations -> Extract Histogram (ligand
protein bind site )

: e-mail:jolin31912811@yahoo.com.tw