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

TL;DR

FragIt is a versatile software tool that uses SMARTS patterns to automate the setup of fragment-based quantum chemical calculations for large molecular systems, lowering the expertise barrier.

Contribution

The paper introduces FragIt, a general fragmentation tool that automates input file preparation for quantum chemical calculations using SMARTS patterns, applicable to diverse molecular systems.

Findings

Successfully automates setup for large systems

Supports proteins, DNA, and polysaccharides

Easily extendable to other methods

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.