Computational chemistry and organic synthesis
Types of coordinates,
z-matrices, input files
How to locate a
Transition State
Programs used, file
formats and conversion
Literature and pointers
to WWW sites
The reaction coordinate and the potential energy surface Path or line searches in MOPAC Quantum chemistry MOPAC, AMPAC, VAMP Literature
Normal coordinates Grid searches in MOPAC Frontier Molecular Orbital theory Gamess, Spartan WWW sites
Internal coordinates The MOPAC Saddle algorithm Solvent effects Sybyl, MacroModel
Applying symmetry and dummy atoms From MOPAC to Gamess Electrostatic effects MOLDEN
Creating MOPAC input files Babel
Creating Gamess input files

To see which file belongs where, there is a (~1000 x 750) picture with an overview.
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