Abstract

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]. In fragmentation methods, a large system is divided into several smaller subsystems called fragments. Each fragment is treated with some ab initio level of theory and different methods [2]–[7] include the surrounding environment in different ways. In this work, 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. In the FMO method, each fragment is polarized by the presence of the Coulomb field of all other fragments. The underlying equations allow for a systematic improvement of the energy by considering pairs and optionally triples of fragments [10], the latter often within milihartree accuracy of the corresponding ab initio energy. FMO supports correlated treatment of one or more fragments [11]–[13] as well the possibility of obtain excitation energies with good accuracy. [14] The FMO method in GAMESS [15] utilizes a novel parallelization scheme [16] to allow computations to be carried out efficiently on desktop computers as well as large scale super computers. [17] Fragmentation can occur across covalent bonds using either the Hybrid Orbital Projection (HOP) [18] or Adapted Frozen Orbital (AFO) [19], [20] method. The EFMO method, also available in GAMESS, neglects the Coulomb bath from FMO and replaces it with classical terms to improve the computational speed to Prepare Input Files for Fragment Based Quantum Chemical Calculations for in silico drug-target flexibility complement methodology-design for the generation of a peptide-mimic novel pharmacoelement binding to the active loop of a Haemophilus influenzae porin P2 amino acid conserved sequences.

Keywords

rational Tool; Input Files; Fragment Based; Quantum Chemical Calculations; drug-target flexibility; complement methodology-design; peptide-mimic; novel pharmacoelement; active loop; Haemophilus influenzae; porin P2; amino acid; conserved sequences.