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
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:
- When a molecule is loaded and there is no bonding
connectivity data provided: e.g., a Gaussian input file without Geom=Connectivity, a log file (since these files
don’t have bonding connectivity data in general), a PDB file for which Standard Bonding for Residues is not requested
or for included HETATMS when CONECT records are either not present or
are requested to be ignored, and so on.
- When you select.
- When you perform point group or space group based
symmetrization with the option checked.
- When you click Combine Cells
or select in
the PBC dialog.
- When you click Apply
or OK in the Custom
Bonding Parameters dialog. In this case, GaussView will
recalculate bonding for any atom pairs that have custom bonding
parameters. Important Tip: If any atoms are
currently selected, consideration for rebonding will occur only for
them. Otherwise, consideration will be given to all atoms.
The fields in the dialog have the following meanings:
- Active?: Whether the
parameter is active (applied).
- Elem. 1 and Elem. 2: Atoms involved in the bond.
- Triple, Double, Resonant, Single, Weak:
Maximum bond length for the specified bond type. Weak bonds are
represented by a single dashed line. They can be visually useful for
representing things like hydrogen bonds, and its value is typically
left at 0. In this case, atoms separated by distances greater than the
single bond value are treated as unbonded.
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).