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 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.
Highlights
The need to compute molecular properties for larger and larger systems with desirable accuracy has led to the development of novel methods such as fragmentation methods [1]
We are interested in setting up Fragment Molecular Orbital (FMO) [5,6] and Effective Fragment Molecular Orbital (EFMO) [8,9] calculations, but our method is extensible to other fragment based methods
[17] Fragmentation can occur across covalent bonds using either the Hybrid Orbital Projection (HOP) [18] or Adapted Frozen Orbital (AFO) [19,20] method
Summary
The need to compute molecular properties for larger and larger systems with desirable accuracy has led to the development of novel methods such as fragmentation methods [1]. FragIt can be extended to write input files for other (fragment) methods and new patterns of fragmentation can be created and tested without changing the source code.
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