Friday, May 25, 2012

New paper: FragIt; A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

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.

Abstract
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.
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