Regardless of the coordinate system used in defining the geometry, if XYZ is present, then all atoms will be converted to Cartesian coordinates, and the calculation will be run entirely in Cartesian coordinates.
When a system involving several rings, or big rings, is optimized using
internal coordinates, the geometry optimizers often have difficulty. This
is because the effect of a small change in an angle can be a large change in the
interatomic distance of two bonded atoms. This is particularly important
in enzymes and other large molecules. This problem is completely solved if
Cartesian coordinates are used. Therefore, if problems are encountered
with geometry optimizations, particularly if internal coordinates are used,
keyword XYZ should be used.
If XYZ is used, the optimization flags are not changed.
Therefore, before running a system with XYZ all the
optimization flags should be set to "1". For atoms 1, 2, and 3, the
optimization flags are forced to 1 if all the other optimization flags are set
to 1. To be safe, use XYZ with 0SCF, then
edit the resulting ARC file to delete XYZ and set the
optimization flags by hand.
Be very careful if some atoms have optimization flags set to"0". If
the geometry supplied is in internal coordinates, and an atom, say atom 10,
has all three optimization flags set to "0", then that means "Do not change
the bond length, angle, and dihedral of atom 10, with reference to the atoms
used for the connectivity." The atom can still move if the atom it is
attached to moves. If that atom is converted to Cartesian coordinates,
the optimization flags will still be zero, but now the definition changes to
"Do not change the Cartesian coordinates of atom 10." This is very
different from the internal coordinate definition.
Any dummy atoms are automatically deleted if XYZ is
present. Dummy atoms are only meaningful if internal coordinates are