To calculate energy, build a molecular surface and for all energy operations you need to convert a PDB file into an ICM object.

• MolMechanics/ICM-Convert/Protein
• Select the object you want to convert from the drop down list.
• Check or uncheck the options, delete water, optimize hydrogens, replace the original, and/or display the result.

To convert a small molecule into an ICM object.

• MolMechanics/ICM-Convert/Chemical
• Select the ligand.
• Choose whether you want to keep the current geometry of the ligand or not.
• Check or uncheck the options build hydrogens, fix amide bonds, and/or overwrite geometry.