May 11 2023
As an example we will use the kinase structure 1xbb.
- Click on the search tab and type 1xbb.
- Click on the ligedit tab
- Click on the Setup Ligand button.
- Enter the ICM selection language for the Ligand Molecule (a_1xbb_asti) or use the drop down button to locate it.
- Select whether or not you would like ICM to automatically assign formal charges and set the pH.
- Select the Receptor Setup button.
- Enter the ICM selection language for Receptor Object (a_1xbb.) or use the drop down button to locate it.
- Select whether or not you wish to keep all waters in the receptor, keep tight waters, delete all waters, optimize existing hydrogens and optimize His, Pro, As, Gln, and Cys. The "mask" option will hide atoms not reported in the crystal strucure (e.g. occupancy 0). If this box is not checked ICM will build the missing atoms of the side-chain.
- Click on the option to select Box Around Existing Ligand. There are other options: Identify Pocket Box will run ICMpocketFinder and return a table of pockets. Click on the table to select the pocket you want and then press OK. You can also Make Box Around Atom Selection.
- Enter a box margin of 3. This option defines the size of the energy maps around the ligand. The value of 3. should encompass the whole site but if you have a binding pocket that is very elongated or unusual in any way it is recomended that you check that the purple box covers the site you are interested in.
- At this stage you can change the size of the box by dragging on the corners of the purple box in the graphics display. Generally the default box is the appropriate size so no changes are needed.
- Click OK and the energy maps will be generated.
- Once everything is setup you will see the ligand and receptor objects along with the original pdb file in the ICM workspace.
- If the ligand-receptor complex is a PDB structure and hydrogens have been added and optimized then it is important to run a minimization after setup.