Casper very recently submitted this paper to PLoS ONE and deposited it at arxiv.org
The use of fragmentation methods to treat very large systems is currently somewhat troublesome due to the complexity of the input files these programs require. We've made a tool called FragIt to generate run-ready input files which lowers the barrier of entry into this fragmented world.
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
for support, setup and lower the barrier of entry for usage by
non-experts. We present a fragmentation methodology and accompanying
tools called FragIt to help setup these calculations. It uses the SMARTS
language to find chemically appropriate substructures in structures and
is used to prepare input files for the fragment molecular orbital
method in the GAMESS program package. We present patterns of
fragmentation for proteins and polysaccharides, specifically
D-galactopyranose for use in cyclodextrins.
The source code is available at github. You can also try out a web-version at www.fragit.org.