[ His,Asn,Gln and Pro ]

Sometimes it is necessary to have a PDB file in the form of a true ICM-object for which you may calculate energy, build a molecular surface and perform all operations. There are two ways of converting a PDB file into an ICM object.

OPTION 1:

• Right click on the name of the protein, displayed in red, in the ICM workspace panel and a menu will be displayed.
• Select ConvertPDB in the menu and the following data entry box will be displayed as shown below.

OPTION 2 a more rigorous conversion in ICM-PRO:

• Select MolMechanics/Convert/Protein and the following data entry box will be displayed as shown below.

Six options can be selected:

1. Delete water molecules if you are not interested in them.
2. Optimize hydrogens if you wish but this may take time.
3. Delete the original PDB file and replace it with the converted ICM object.
4. Undisplay during conversion will speed up the conversion procedure.
5. You can display the final converted object if you wish.
6. Running the conversion in the background will speed the procedure up.

It is sometimes important to check the orientation of amino acid residues such as His, Gln and Asn. For example the orientation of the heavy atoms of Asn, Gln and His and uncertainitly in the protonation of His. The optimize H, His, Asn, Gln Pro option can do this for you by maximizing hydrogen bonds and other interactions with the rest of the protein and/or with the ligand.

To perform this optimization

• Convert your protein to an ICM Object.
• Select MolMechanics/Optimize, H, His,Asn,Gln and Pro