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How to save a PDB file of just the native ligand from the experimental structure, so you can overlay the native ligand structure with the docked ligand.

Overlaying the docked poses with the native ligand

Using ViewDock to look at the scores and poses of docked small molecule ligands in the target receptor

Alternate way to select and delete a ligand from a protein structure - using the Cntrl + Left Click selection strategy

Deleting the existing/experimental ligand from the structure before docking

Draw the "box" in AutoDock Vina. Use a native or experimental ligand to help you locate and size the box.

Open AutoDock Vina, specify receptor, ligand and output location

Add a ligand to the Chimera session with the dock-prepped protein/receptor structure

Saving the Chimera session. Don't forget to type out a .py suffix for your file name.

Dock Prep of the Protein structure including charges

Selecting and hiding protein chains and small molecules

Saving the structure as Chem3D and *.pdb files

Adding a formal charge

Checking bond lengths and angles, optional MM2 calculation

Drawing a structure in Chem3D