Refinement of the amber force field for nucleic acids. Improving the description of / conformers

¹ University of Barcelona
² Academy of Sciences of the Czech Republic
³ University of Utah
⁴ University of Nottingham

^* To whom correspondence should be addressed. E-mail: modesto{at}mmb.pcb.ub.es.

Submitted on September 19, 2006
Revised on November 20, 2006
Accepted on 5 February 2007

	Abstract

We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the / concerted rotation in nucleic acids. The modified force-field corrects over-populations of the /=(g⁺,t) backbone which were seen in long (more than 10 ns) simulations with previous AMBER parameter sets (parm94-99). The force field has been derived by fitting to high-level quantum mechanical (QM) data and verified by comparison with very high-level QM calculations and by a very extensive comparison between simulations and experimental data. The set of validation simulations includes two of the longest trajectories published to date for the DNA duplex (200 ns each) and the largest variety of nucleic acids structures studied to date (15 different nucleic acids families and 97 individual structures). The total simulation time used to validate the force field includes near 1 µs of state-of-the-art molecular dynamics simulations in aqueous solution.

Key Words: Alfa-gamma, DNA, Molecular Dynamics, Simulation, Supercomputation

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