Molecular Dynamics Simulations of HADDOCK-predicted Complex Structures of apoE2 and Factor H

Input and output data for the molecular dynamics simulations of the FH5–7/ApoE2 complex. Initial structures generated with the HADDOCK v2.4 web server with 3 nm distance restraints for lysine pairs that were experimentally found to be cross-linked with DSS. Five clusters and the four representative structures provided by HADDOCK were then used for atomistic molecular dynamics simulations. These structures were solvated and simulated with both CHARMM36m and Amber FF14SB force fields for 250 ns each using GROMACS 2021. The recommended simulation parameters were used for both force fields, and they are available in the mdp files. For each of these 5 (clusters) x 4 (structures per cluster) x 2 (force fields) = 40 simulations, the outputs and inputs are provided; the trajectory (xtc), energy file (edr), final structure (gro), run parameter file (tpr), and continue point (cpt) are system-specific, whereas a single topology (top) and index file (ndx) is shared among all simulations with the same force field. The molecule definitions (itp) referred to in the topology are provided in the compressed files.本数据集为FH5–7/ApoE2复合物的分子动力学模拟输入输出数据。初始结构通过HADDOCK v2.4服务器生成，针对实验中经DSS交联的赖氨酸残基对设置了3 nm的距离约束。随后选取该服务器给出的5个聚类结果与4个代表性结构，对其进行溶剂化处理后，结合CHARMM36m与Amber FF14SB两种全原子力场，使用GROMACS 2021软件完成时长为250 ns的全原子分子动力学模拟；两类力场的模拟均采用官方推荐参数，相关mdp参数文件已公开提供。本数据集涵盖5（聚类数）×4（单聚类代表性结构数）×2（力场种类）=40组模拟的输入与输出文件。其中，每组模拟独有的文件包括轨迹文件（xtc）、能量文件（edr）、最终结构文件（gro）、运行参数文件（tpr）以及续算点文件（cpt）；而使用同一种力场的所有模拟将共享一份拓扑文件（top）与索引文件（ndx）。拓扑文件中引用的分子定义文件（itp）已打包在压缩文件中。