Regardless of what type of coordinates are used in the data set, INT
will force all the coordinates to be internal coordinates. Atom 1 is,
by definition, always defined in Cartesian coordinates.
If INT is used, the optimization flags are not changed.
Therefore, before running a system with INT all the
optimization flags should be set to "1", except for atoms 1, 2, and 3.
For atom 1, all optimization flags should be set to "0", for atom 2, the
second and third flags should be "0", and for atom 3 the third flag should be
Be very careful if some atoms have optimization flags set to "0". If
the geometry supplied is in Cartesian coordinates, and an atom, say atom 10,
has all three optimization flags set to "0", then that means "Do not change
the Cartesian coordinates of atom 10." If that atom is converted
to internal coordinates, the optimization flags will still be zero, but now
the definition changes to "Do not change the bond length, angle, and dihedral
of atom 10, with reference to the atoms used for the connectivity." Now
atom 10 will move if the atom it is attached to moves. This is fundamentally
different from the Cartesian coordinate definition.
Any dummy atoms are automatically deleted if INT is
present. This is because the first step in running INT is to
convert the system to Cartesian coordinates. This involved deleting any
dummy atoms. The next step involves conversion from Cartesian to
INT is a rapid and efficient way of deleting atoms from a
molecule that is defined using internal coordinates. Re-label the atoms
to be deleted as dummy atoms, and run INT with 0SCF.