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[ ICM Workspace | Graphical Display ]
If you are going to make any energy calculation in ICM (eg docking, display H-bonds, display electrostatic and binding property surfaces etc..) it is necesary to convert a protein or chemical into an ICM object.
To convert a PDB structure into an ICM object follow the steps shown below:
If your object is an ICM object it will tell you in the ICM Workspace:
h2-- How to Convert a Chemical from the PDB {Convert Chemical} __REQUIRES(E)
The protein data bank has not been storing any information about covalent bond types and formal charges of the chemical compounds interacting with proteins! This oversight makes it impossible to automatically convert those molecules to anything sensible and requires your manual interactive assignment of bond types and formal charges for each compound in a pdb-entry. Therefore, if you apply the convert command to a pdb-entry with ligands, the ligands will just become some crippled incomplete molecules that can not be further conformationally optimized.
Therefore, follow these steps to convert a chemical properly from a pdb form to a correct icm object. There are two ways to do this either via the ICM Workspace (recommended) or via the Graphical Display.
4.2.1 Converting a Chemical from the PDB using the ICM Workspace |
Change bond orders:
NOTE: Keyboard shortcuts are provided to make editing faster. |
Change atom and charge:
NOTE: Keyboard shortcuts are provided to make editing faster. |
Convert to 3D in MMFF force field:
NOTE: If you need to add an extra bond you will need to use the full molecular editor. Right click on the name of the ligand in the ICM Workspace and select Edit/Edit Compound. |
4.2.2 How to Convert a Chemical from the PDB using the Graphical Display |
To change the bond types in your ligand:
You can either select (see selection menu section)the atoms you wish to change graphically using the rectangular or lasoo selection button OR
You can select the By two atoms tabs and right click on the atoms you wish to change and then selecting the atom descriptor with the left mouse button as shown below.
To set the formal charge of a compound:
Click on MolMechanics/Edit Structure/Set Formal Charge and then select the appropriate charge.
The final step is to convert the compound into an ICM object:
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