Kaiso-meDNA systems

This list contains the pdb, psf and dcd files of 7 different systems. The MeCG2, MeCG2_mutCG, MeECad, MeECad_mod and MeECad_mod_mutTA systems have three replica runs of length 600 ns or 400ns. The MeCG2_E535A and MeECad_mod_mutTA systems each have a single run of 200 ns. Note: sequences with a C/G pair in the 5'-flanking site: MeCG2_mutCG, MeECad, MeECad_mod; Sequences with a T/A pair in the 5'-flanking site: MeCG, MeECad_mod_mutTA. The trajectories uploaded here are saved at 1 ns/frame (i.e. 600 frames = 600 ns). The systems are pbc-wrapped and aligned for protein. Trajectories that are not pbc-wrapped and saved more frequently at 0.2 ns/frame (i.e. 5x as many frames) are available upon request. To load the trajectories in VMD: <pre><code>mol new 01_MeCG2.psf mol addfile 01_MeCG2_run1.dcd waitfor all</code></pre>本数据集包含7种不同模拟体系的pdb、psf与dcd文件。其中，MeCG2、MeCG2_mutCG、MeECad、MeECad_mod及MeECad_mod_mutTA体系均包含3组重复模拟运行，单组模拟时长为600纳秒或400纳秒；MeCG2_E535A与MeECad_mod_mutTA体系则仅包含1组时长为200纳秒的模拟运行。 注：5'侧翼区域存在C/G碱基对的体系包括MeCG2_mutCG、MeECad及MeECad_mod；5'侧翼区域存在T/A碱基对的体系包括MeCG、MeECad_mod_mutTA。 本次上传的轨迹文件均以1纳秒每帧的频率保存（即600帧对应600纳秒的模拟时长）。所有体系均经过周期性边界条件（PBC）包裹处理，并针对蛋白质分子完成了轨迹对齐。 如需未经过PBC包裹、且以0.2纳秒每帧的更高频率保存（帧数为原文件的5倍）的轨迹文件，可联系申请获取。 若需在VMD软件中加载轨迹，可使用如下命令： <pre><code>mol new 01_MeCG2.psf mol addfile 01_MeCG2_run1.dcd waitfor all</code></pre>