The assignment of fragments to individual layers usually based on the distance to a point of interest, is also no minor task when you have hundreds of fragments. Consider also the case of multiple layers which the FMO method supports in similar spirit to the ONIOM method, where one (or several) lower level layer(s) are used for some chemically irrelevant parts of a system but their effect on a higher level layer, which is used for the chemically interesting part, is needed. For example, setting up a fragment calculation on a simple system consisting of three water molecules is feasible to prepare manually, but a protein with thousands of atoms is not. Different systems have different complexities.
#INTENTIONAL FRAGMENT EXAMPLES MANUAL#
Fragmentation across covalent bonds adds more complexity: One must now also consider chemically reasonable places of fragmentation (do not break conjugation, etc.) which itself requires manual inspection of the structure of interest. For a molecular cluster, each individual molecule can be considered a single fragment, for polymers a sub-unit of that polymer could make up a fragment whereas for proteins each individual residue can be considered a fragment. the atom indices that make up the fragment which might not be in any specific order in an input coordinate file, the integer fragment charges and level of theory. The reason for this complexity is that complete knowledge about the individual fragments of interest are required, i.e. Often, the input files for the FMO method are more complex than the regular ab initio input files.
The input to EFMO and FMO are largely identical. The EFMO method, also available in GAMESS, neglects the Coulomb bath from FMO and replaces it with classical terms to improve the computational speed. Fragmentation can occur across covalent bonds using either the Hybrid Orbital Projection (HOP) or Adapted Frozen Orbital (AFO), method. The FMO method in GAMESS utilizes a novel parallelization scheme to allow computations to be carried out efficiently on desktop computers as well as large scale super computers. FMO supports correlated treatment of one or more fragments – as well the possibility of obtain excitation energies with good accuracy. The underlying equations allow for a systematic improvement of the energy by considering pairs and optionally triples of fragments, the latter often within milihartree accuracy of the corresponding ab initio energy. In the FMO method, each fragment is polarized by the presence of the Coulomb field of all other fragments. In this work, we are interested in setting up Fragment Molecular Orbital (FMO), and Effective Fragment Molecular Orbital (EFMO), calculations, but our method is extensible to other fragment based methods. Each fragment is treated with some ab initio level of theory and different methods – include the surrounding environment in different ways. In fragmentation methods, a large system is divided into several smaller subsystems called fragments. 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. 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. We present SMARTS patterns of fragmentation for proteins, DNA and polysaccharides, specifically for D-galactopyranose for use in cyclodextrins.
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 a general fragmentation methodology and accompanying tools called FragIt to help setup these calculations. Previous tools relies on specific annotations in structure files for automatic and successful fragmentation such as residues in PDB files.
#INTENTIONAL FRAGMENT EXAMPLES SOFTWARE#
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. However, it remains difficult to set up these calculations without expert knowledge. 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.
0 kommentar(er)
