Custom Bonding Parameters

The Custom Bonding Parameters are used in those circumstantces when GaussView determines bonding based on geometry: distances between atoms. You can specify them for the current molecule via the Tools=>Custom Bonding Parameters menu path or by default in the Custom Bonding Parameters Preferences.

Note that this is an advanced GaussView feature intended for experienced users. Caution is in order when using it.


Defining Custom Bonding Parameters

GaussView determines bonding based on geometry in the following cases:

The fields in the dialog have the following meanings:

The custom bonding parameters don’t affect molecule building; builder fragments come with bonding provided. Since bonding can affect MM atom type determinations, adding hydrogens, chirality determinations, and the like, changing the bonding parameters can have real consequences when the bonding ends up being different than it would by default. These parameters are useful when GaussView doesn’t assign some bonds in the expected way because of an unusual or otherwise poor geometry (e.g., a PDB resulting created from a low resolution X-Ray diffraction experiment).