[ Covalent Docking ]

To dock from a table in the ligand editor.

• Setup the ligand and receptor in the ligand editor.
• Read in the sdf file or chemical spreadsheet which contains the chemicals you wish to dock.
• Select the Advanced button in the ligand editor and select Dock Table.
• In the dialog box select the thoroughness (length of simulation) and the number of conformations.

To undertake covalent docking from a table:

Read in the PDB file you wish to dock to containing the covalently linked ligand.

Setup the ligand in the ligand editor.

Setup the receptor in the ligand editor.

Pick a hydrogen atom in the ligand to attach a modifier and pick any atom in the modified residue. Next, click on the Advanced button and choose "Define Covalent Ligand".

Open the molecular editor. Note you may first need to click on the display tab to see the Molecular Editor button.

Sketh the reactant and product.

Two of the atoms need to be labeled to match the residue in the receptor.

Append the reaction to a chemical table. Note more than one reaction can be added to the table to match the ligands in your chemical table that you wish to dock.

Load the chemical table containing the ligands you wish to dock.

Choose Advance/Dock Table and select the covalent options shown.