  Near linear scaling fragment based quantum chemical calculations are becoming
increasingly popular for treating large systems with high accuracy and is an
active field of research. However, it remains difficult to set up these
calculations without expert knowledge. To facilitate the use of such methods,
software tools need to be available to support these methods and help to set up
reasonable input files which will lower the barrier of entry for usage by
non-experts. Previous tools relies on specific annotations in structure files
for automatic and successful fragmentation such as residues in PDB files. We
present a general fragmentation methodology and accompanying tools called
FragIt to help setup these calculations. FragIt uses the SMARTS language to
locate chemically appropriate fragments in large structures and is applicable
to fragmentation of any molecular system given suitable SMARTS patterns. We
present SMARTS patterns of fragmentation for proteins, DNA and polysaccharides,
specifically for D-galactopyranose for use in cyclodextrins. FragIt is used to
prepare input files for the Fragment Molecular Orbital method in the GAMESS
program package, but can be extended to other computational methods easily.
