作者
Alberto Pérez, Iván Marchán, Daniel Svozil, Jiri Sponer, Thomas E Cheatham, Charles A Laughton, Modesto Orozco
发表日期
2007/6/1
期刊
Biophysical journal
卷号
92
期号
11
页码范围
3817-3829
出版商
Elsevier
简介
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 α/γ concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the α/γ=(g+,t) backbone that were seen in long (more than 10ns) 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 (200ns 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 …
引用总数
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