| Prev | 19.1 Setup Ligand and Receptor | Next |
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 waters in the receptor, optimize existing hydrogens and optimize His, Pro, As, Gln, and Cys.
- Click on the option to select Box Around Existing Ligand. There are other options: Identify Pocekt 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.
- Click OK and the energy maps will be generated.
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