Developments and applications of ABINIT-MP software based on the fragment molecular orbital method

Tatsuya Nakano, Yuji Mochizuki, Kaori Fukuzawa, Shinji Amari, Shigenori Tanaka

Research output: Chapter in Book/Report/Conference proceedingChapter

28 Citations (Scopus)

Abstract

The fragment molecular orbit (FMO) method relies on the division of a large molecular system into a collection of small fragments and on the molecular orbital (MO) calculations for the fragments (monomers) and their pairs (dimers) performed to obtain the total energy and other molecular properties. The ABINIT-MP software is a program code freely available on the web to perform the FMO calculations for biopolymers, such as proteins and nucleic acids. The chapter focuses on the recent developments of the ABINIT-MP software and some examples of its application to the MO calculations for proteins. The FMO calculations in the Hartree-Fock , the second-order Møller-Plesset perturbation , and the configuration interaction with singles approximations are now available in an efficiently parallelized fashion. The application examples are demonstrated for the virtual screening of ligand molecules for estrogen receptor and the evaluation of the excitation energy of photoactive yellow protein. ABINIT-MP software is developed to make ab initio calculations for biomolecules more efficient.

Original languageEnglish
Title of host publicationModern Methods for Theoretical Physical Chemistry of Biopolymers
PublisherElsevier
Pages39-52
Number of pages14
ISBN (Print)9780444522207
DOIs
Publication statusPublished - 2006
Externally publishedYes

ASJC Scopus subject areas

  • Chemistry(all)

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