TY - CHAP
T1 - Developments and applications of ABINIT-MP software based on the fragment molecular orbital method
AU - Nakano, Tatsuya
AU - Mochizuki, Yuji
AU - Fukuzawa, Kaori
AU - Amari, Shinji
AU - Tanaka, Shigenori
N1 - Funding Information:
This work was supported by the ‘Frontier Simulation Software for Industrial Science’ project of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and by the Core Research for Evolutional Science and Technology (CREST) project of the Japan Science and Technology Agency (JST).
PY - 2006
Y1 - 2006
N2 - 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.
AB - 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.
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U2 - 10.1016/B978-044452220-7/50066-6
DO - 10.1016/B978-044452220-7/50066-6
M3 - Chapter
AN - SCOPUS:84882856060
SN - 9780444522207
SP - 39
EP - 52
BT - Modern Methods for Theoretical Physical Chemistry of Biopolymers
PB - Elsevier
ER -