PDBs and GROMACS xtc trajectories for DNA aptamers on SARS-CoV-2 spike protein

The gzipped tar file contains the initial configurations from docking for the 8_1, 10_1 and 12_1 structures of the two DNA aptamers interacting with the receptor binding domain of the SARS-CoV-2 spike protein; the clusters from a long MD trajectory for the 10_1 structure; sample trajectories in GROMACS compressed xtc format for the 3 structures; the reconstructed trajectory from umbrella sampling simulation in xtc format for the 10_1 (note: in order to plot xtc trajectories, a GROMACS configuration file must first be reconstructed from the PDB, with the GROMACS utility pdb2gmx).本gzip压缩tar归档文件包含两种与严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）刺突蛋白受体结合域（receptor binding domain, RBD）相互作用的DNA适配体（DNA aptamer）的8_1、10_1及12_1结构的分子对接初始构象；包含10_1结构的长分子动力学（Molecular Dynamics, MD）轨迹所得到的构象聚类簇；包含三种结构的GROMACS压缩xtc格式样本轨迹；以及10_1结构的伞形采样（Umbrella Sampling）模拟重构xtc轨迹。（注：若需绘制xtc轨迹，需先借助GROMACS工具pdb2gmx从PDB文件中重构GROMACS配置文件。）