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标题: 求助：如何计算蛋白A链的RMSD [打印本页]

作者
Author: lucky2023 时间: 2023-7-19 16:04
标题: 求助：如何计算蛋白A链的RMSD
蛋白有A链和B链，准备分析A链在模拟中相对于第一帧A链的RMSD变化。
我定义了一个只有A链的组，之后输入命令 gmx rms -s em.tpr -f md_noPBC.xtc -o 1-5ntdrmsd.xvg -n 1dx5ntdss.ndx -tu ns，选项应该怎么选呢？
如果最小二乘法拟合Cα的话，是否要定义一个只有A链Cα的组？
Command line:
  gmx rms -s em.tpr -f md_noPBC.xtc -o 1-5ntdrmsd.xvg -n 1dx5ntdss.ndx -tu ns

Reading file em.tpr, VERSION 2020.3 (single precision)
Reading file em.tpr, VERSION 2020.3 (single precision)
Select group for least squares fit
Group    0 (       System) has  8966 elements
Group    1 (       Protein) has  8966 elements
Group    2 (    Protein-H) has  4533 elements
Group    3 (       C-alpha) has 579 elements
Group    4 (    Backbone) has  1737 elements
Group    5 (    MainChain) has  2314 elements
Group    6 ( MainChain+Cb) has  2858 elements
Group    7 ( MainChain+H) has  2858 elements
Group    8 (    SideChain) has  6108 elements
Group    9 ( SideChain-H) has  2219 elements
Group 10 ( a_7565-8966) has  1402 elements
Select a group: 4
Selected 4: 'Backbone'
Select group for RMSD calculation
Group    0 (       System) has  8966 elements
Group    1 (       Protein) has  8966 elements
Group    2 (    Protein-H) has  4533 elements
Group    3 (       C-alpha) has 579 elements
Group    4 (    Backbone) has  1737 elements
Group    5 (    MainChain) has  2314 elements
Group    6 ( MainChain+Cb) has  2858 elements
Group    7 ( MainChain+H) has  2858 elements
Group    8 (    SideChain) has  6108 elements
Group    9 ( SideChain-H) has  2219 elements
Group 10 ( a_7565-8966) has  1402 elements

作者
Author: sobereva 时间: 2023-7-20 12:30
取决于你的目的，如果你就是指想靠alpha-C原子体现A链的骨架结构波动，那就对A链的这些原子专门定义一个组就完了，然后gmx rms里两次都选这个组

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