Supporting files for the article "Magic methyl effect in RNA catalysis: how tandem ribose 2'-O-methylation in the active site accelerates RNA-catalyzed RNA methylation"

Supporting files for the article "Magic methyl effect in RNA catalysis: how tandem ribose 2'-O-methylation in the active site accelerates RNA-catalyzed RNA methylation". The deposition contains: 1. Classical MD input files: a. Gromacs input files for performing classical molecular dynamics along with necessary structure (.gro) and topology (.top) files, based on the Amber force fields, for the MTR1wt (labelled wt) and MTR1m2 system (labelled 2met). 2. Classical MD production run trajectories used for creating figures in the manuscript (related gro files are included in classicalMD.tar.gz). 3. QM/MM MD input files: a. cp2k input files and basis sets for running unbiased density functional theory (DFT) quantum mechanics (QM)/ molecular mechanics (MM) molecular dynamics (MD) simulations for the MTR1wt (labelled wt) and MTR1m2 system (labelled 2met). b. cp2k and plumed input files for performing QM/MM metadynamics to obtain the free energy profile as a function of U42/Um42 pseudorotational angle. c. cp2k input files for simulating the methylation reaction in MTR1wt and MTR1m2 with QM/MM metadynamics.本数据集为论文《RNA催化中的神奇甲基效应：活性位点内串联核糖2'-O-甲基化如何加速RNA催化的RNA甲基化》的配套支持文件。本次提交的内容包含： 1. 经典分子动力学（Classical MD）输入文件： a. 基于Amber力场，针对MTR1wt（标记为wt）和MTR1m2系统（标记为2met），用于开展经典分子动力学模拟的Gromacs输入文件，以及必要的结构文件（.gro）和拓扑文件（.top）。 2. 用于制作论文稿件配图的经典分子动力学生产模拟轨迹文件（相关gro文件已包含在classicalMD.tar.gz压缩包中）。 3. 量子力学/分子力学（QM/MM）分子动力学（MD）输入文件： a. 针对MTR1wt（标记为wt）和MTR1m2系统（标记为2met），开展无偏密度泛函理论（DFT）量子力学/分子力学分子动力学模拟所需的CP2K输入文件与基组文件。 b. 用于通过QM/MM元动力学模拟获取以U42/Um42假旋转角为变量的自由能分布曲线所需的CP2K与PLUMED输入文件。 c. 针对MTR1wt与MTR1m2系统，通过QM/MM元动力学模拟甲基化反应所需的CP2K输入文件。