Edit Menu

The Edit menu modifies molecular properties such as atomic mass (isotope), connectivity, bond orders, formal charges, and charge groups, which are required for developing or using force fields. These tasks are often useful for imported models that may have topology data different from DFF.

• Isotope sets atom masses of isotopes for the currently selected model. This command can change a single atom or all atoms of the same element in a model. Click to open a dialog. In the dialog, select an atom with a mouse click, choose the scope of application and atom mass, then click Execute.

• Add Hydrogen adds hydrogen atoms using the standard octet rule. This is often useful for imported models that do not have explicit hydrogen atoms.

• Bond Order sets the connectivity and bond orders of the selected models. You can optionally keep existing connectivity or rebuild connectivity before calculating the bond orders.

• Formal Charge assigns or removes formal charges. Assignment can be automatic or manual. For automatic assignment, existing values are removed by default; optionally, existing formal charges can be protected. The manual option is useful for assigning special formal charges, either by atom or by atom type.

• Torsion Angle sets or modifies torsion angles in a dialog. Select four atoms consecutively that define a dihedral angle. A new angle can then be set, or an existing one can be rotated by a specified value. Clicking Execute performs the specified function. If Make new model(s) is selected, each Execute generates a new model with the specified torsion angles.

• Improper Torsion Angle is similar to the torsion command, but sets or modifies improper torsion angles. In the dialog, select four atoms that define an improper dihedral angle. Improper torsion can be defined for four atoms with one center atom bonded to the other three. Definitions of improper dihedral angles can differ; usually select the out-of-plane atom as the first atom and the center atom as the second.

• Reset COM resets the center of mass for a model. Relative positions of atoms are not altered and energy calculations are not impacted. Reset COM is useful for obtaining a better view of the model, especially when the model needs to be rotated on the screen.

• Charge Group defines charge groups in a molecule model as often required by simulation engines. This method can be used only after a force field has been assigned. It works by querying the charge separation between any two bonded atoms. If the charge crossing a bond is smaller than an adjustable threshold, the bond is used as a division between two charge groups. Execute begins the calculation, and the results are displayed in the center panel.