Hundred nanosecond molecular dynamics simulation of the G domain of K-Ras4B

(This is a public copy of https://figshare.com/s/453b1b215cf2f9270769) This is a one hundred nanosecond simulation of the G domain of K-Ras4B (UNIPROT:P01116-2, residues 1-166). The simulation was generated using GROMACS v.4.6.5 with the AMBER99SB-ILDN forcefield (altered following doi:10.1002/jcc.10262, see References), TIP3P water and 0.15 M salt. The leap-frog integrator with 2 fs timestep was used. A v-rescale thermostat was used at 310 K, with two energy groups (protein+GTP+MG and water+salt) and a time constant of 0.1 ps. PME was used with a tolerance of 1e-5 for the coulomb interactions and a cutoff was used for the VdW interactions, both with a cutoff of 1.1 nm. A Parrinello-rahman barostat was applied with a reference pressure of 1 bar and a time constant of 1 ps. For more information take a look at md.mdp. Coordinates were saved every 1 nanosecond and waters were stripped, resulting in a trajectory of 101 snapshots. The initial model was made using the G-domain of GppNHp bound H-Ras (PDB ID: 4EFL). The protein was converted using MODELLER v9.16(doi:10.1002/cpbi.3 , see References) and GppNHp was converted to GTP by hand.

(本内容为https://figshare.com/s/453b1b215cf2f9270769的公开副本) 本数据集为K-Ras4B的G结构域（通用蛋白质资源库（UniProt）:P01116-2，残基范围1-166）的100纳秒分子动力学模拟结果。本次模拟采用GROMACS v.4.6.5软件完成，力场选用AMBER99SB-ILDN（已按doi:10.1002/jcc.10262进行调整，详见参考文献），溶剂体系采用TIP3P水，盐浓度设置为0.15 M。模拟采用跳蛙（leap-frog）积分器，时间步长为2 fs。温控环节使用v-rescale温控器维持体系温度310 K，将体系划分为两组能量群体：蛋白质+GTP+镁离子与水+盐，温控时间常数设为0.1 ps。长程静电相互作用采用粒子网格Ewald（PME）方法计算，精度阈值为1×10^-5；范德华（Van der Waals, VdW）相互作用采用截断方式处理，两类相互作用的截断半径均为1.1 nm。压力调控采用Parrinello-Rahman压浴器，参考压力设置为1 bar，压力调控时间常数为1 ps。更多细节可查阅md.mdp文件。模拟轨迹的坐标每1纳秒保存一次，且在保存时剔除了水分子，最终得到包含101帧快照的轨迹文件。初始模型基于结合GppNHp的H-Ras G结构域（蛋白质数据库（Protein Data Bank, PDB）ID: 4EFL）构建；通过MODELLER v9.16（doi:10.1002/cpbi.3，详见参考文献）完成蛋白质结构转换，并手动将配体GppNHp转换为GTP。