Note

This website is presently under development. The primary website for MOPAC is still http://openmopac.net until the majority of its contents have been migrated here.

XYZ

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.

Notes

  • 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 used.

See also `INT <int.html>`__