Force field parameters for rotation around chi torsion axis in nucleic acids.
To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.
Ode
Hirotaka
H
Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.
Matsuo
Yuri
Y
Neya
Saburo
S
Hoshino
Tyuji
T
D003198:Computer Simulation; D006860:Hydrogen Bonding; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D011789:Quantum Theory; D013816:Thermodynamics
D009696:Nucleic Acids