SIRAH-CoV2 initiative: co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ)

This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. The files 6WIQ_SIRAHcg_rawdata_0-5us.tar, and 6WIQ_SIRAHcg_rawdata_5-10us.tar, contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at www.sirahff.com. Additionally, the file 6WIQ_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6WIQ_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untar the file 6WIQ_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6WIQ_SIRAHcg_prot.prmtop 6WIQ_SIRAHcg_prot.ncrst 6WIQ_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset is part of the SIRAH-CoV2 initiative. For further details, please contact Florencia Klein ([e-mail]) or Sergio Pantano ([e-mail]).本数据集包含新冠病毒2型（SARS-CoV-2）NSP7辅助因子复合物与NSP8羧基末端结构域的10微秒时长粗粒度分子动力学模拟轨迹（PDB编号：6WIQ）。本次模拟采用SIRAH力场，通过Amber18软件包完成，运行于乌拉圭国家超级计算中心（ClusterUY），模拟条件参考Machado等人2019年发表于《Journal of Chemical Theory and Computation》（简称JCTC）的研究工作，并依据Machado与Pantano于2020年发表于JCTC的研究添加了150 mM氯化钠溶液环境。 文件6WIQ_SIRAHcg_rawdata_0-5us.tar与6WIQ_SIRAHcg_rawdata_5-10us.tar包含了用于在VMD（Visual Molecular Dynamics）中可视化、分析、逆映射（backmap），以及最终使用Amber18或更高版本软件继续运行模拟所需的全部原始数据。使用SirahTools运行、可视化并分析粗粒度轨迹的分步教程可访问www.sirahff.com获取。 此外，文件6WIQ_SIRAHcg_10us_prot.tar仅包含蛋白质坐标信息；而6WIQ_SIRAHcg_10us_prot_skip10ns.tar则每10纳秒保存一帧轨迹。快速查看轨迹的操作步骤如下：1. 解压文件6WIQ_SIRAHcg_10us_prot_skip10ns.tar；2. 通过命令行在VMD中加载轨迹：vmd 6WIQ_SIRAHcg_prot.prmtop 6WIQ_SIRAHcg_prot.ncrst 6WIQ_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl。用户可使用VMD常规绘图方法（如范德华模型、球棍模型等），并按残基类型、元素、原子名称等进行着色。 本数据集属于SIRAH-CoV2研究计划的一部分。如需进一步细节，请联系Florencia Klein（邮箱：[e-mail]）或Sergio Pantano（邮箱：[e-mail]）。