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Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

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 alpha/gamma concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the alpha/gamma = (g+,t) backbone that 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 data and verified by comparison with very high-level quantum mechanical 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 NA structures studied to date (15 different NA families and 97 individual structures). The total simulation time used to validate the force field includes near 1 mus of state-of-the-art molecular dynamics simulations in aqueous solution.

SUBMITTER: Perez A

PROVIDER: S-EPMC1868997 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature

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Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Pérez Alberto A Marchán Iván I Svozil Daniel D Sponer Jiri J Cheatham Thomas E TE Laughton Charles A CA Orozco Modesto M

Biophysical journal 20070309 11

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 alpha/gamma concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the alpha/gamma = (g+,t) backbone that 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 data and verified by compa ...[more]

PMID: 17351000

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Project description:We employ the popular all-atom optimized potential for liquid simulations, OPLSAA, force-field to model 17 different alcohols in the liquid state. Using the standard simulation protocol for few hundred nanosecond time periods, we find that 1-octanol, 1-nonanol, and 1-decanol undergo spontaneous transition to a crystalline state at temperatures which are 35-55 K higher than the experimental melting temperatures. Nevertheless, the crystal structures obtained from the simulations are very similar to those determined by X-ray powder diffraction data for several n-alcohols. Although some degree of deviations from the experimental freezing points are to be expected, for 1-nonanol and 1-decanol, the elevation of the freezing temperature warrants special attention because at room temperature, these alcohols are liquids; however, if simulated by the OPLSAA force-field, they will crystallize. This behavior is likely a consequence of exaggerated attractive interactions between the alkane chains of the alcohols. To circumvent this problem, we combined the OPLSAA model with the L-OPLS force-field. We adopted the L-OPLS parameters to model the hydrocarbon tail of the alcohols, whereas the hydroxyl head group remained as in the original OPLSAA force-field. The resulting alcohols stayed in the liquid state at temperatures above their experimental melting points, thus, resolving the enhanced freezing observed with the OPLSAA force-field. In fact, the mixed-model alcohols did not exhibit any spontaneous freezing even at temperatures much lower than the experimental values. However, a series of simulations in which these mixed-OPLSAA alcohols started from a coexistence configuration of the liquid and solid phases resulted in freezing transitions at temperatures 14-25 K lower than the experimental values, confirming the validity of the proposed model. For all of the other alcohols, the mixed model yields results very similar to the OPLSAA force-field and is in good agreement with the experimental data. Thus, for simulating alcohols in the liquid phase, the mixed-OPLSAA model is necessary for large (7 carbons and above) hydrocarbon chains.

Dataset Information

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Publications

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

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