Sample QM/MM files for "Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH∙∙∙Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell Wall Invertase 1"

This dataset accompanies the manuscript: " Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH∙∙∙Nucleophile in Transition State Stabilization in Arabidopsise thaliana Cell Wall Invertase 1". It contains sample CHARMM input and output files, topologies, and parameters required for QM/MM calculations of reaction in a plant cell-wall invertase. The QM/MM inputs include:1. QM/MM MD simulation2. Energy minimization3. Reaction path calculation (adiabatic mapping)4. Umbrella sampling MD along reaction coordinate (PMF computations) The outputs from QM/MM umbrella sampling MD include:Snapshots of stationary points on the PMF plots in Figure 3A for sucrose hydrolysis catalyzed by a plant cell-wall invertase 1 from Arabidopsise thaliana (see Figure 3 in the main text, DOI: 10.1021/acs.jcim.3c00796)Trajectories from the last 40 ps of 100-ps umbrella sampling simulations

本数据集配套学术论文：《多尺度QM/MM（Quantum Mechanics/Molecular Mechanics）模拟揭示拟南芥（Arabidopsis thaliana）细胞壁蔗糖转化酶1中Asp239与1-OH∙∙∙亲核基团在过渡态稳定中的作用》。本数据集包含用于植物细胞壁蔗糖转化酶内反应的QM/MM计算所需的CHARMM示例输入与输出文件、拓扑文件及参数文件。QM/MM输入内容涵盖：1. QM/MM分子动力学（Molecular Dynamics, MD）模拟；2. 能量最小化；3. 反应路径计算（绝热映射）；4. 沿反应坐标的伞形抽样分子动力学模拟（平均力势（Potential of Mean Force, PMF）计算）。QM/MM伞形抽样分子动力学模拟的输出包括：① 拟南芥来源的植物细胞壁蔗糖转化酶1催化蔗糖水解过程中，正文图3A所示PMF曲线驻点的快照（详见正文图3，DOI: 10.1021/acs.jcim.3c00796）；② 100皮秒（ps）伞形抽样模拟中最后40皮秒的轨迹文件。