求助：amber里如何align多个pdb文件

molly85

各位老师们好，我想问一下，amber里如何将多个pdb,再求其平均结构。
我的目的是将最后500帧的top和crd转化成pdb文件，且将最后500帧的第一帧作为参考结构，align之后形成剩下的499个pdb文件。以下是我的in文件parm com.top

trajin com.crd  frame frame
strip :WAT,Na+,Cl-
trajout com_frame.pdb

rpestana94

You can try with average command in cpptraj, I always get like weird bonds, but you can try https://amberhub.chpc.utah.edu/average/

molly85

rpestana94 发表于 2023-12-22 00:32
You can try with average command in cpptraj, I always get like weird bonds, but you can try https:// ...

rpestana94老师，这个是求平均结构的命令？那我如何align多个pdb文件，是否可以使用rms frame mass？

rpestana94

molly85 发表于 2023-12-21 23:05
rpestana94老师，这个是求平均结构的命令？那我如何align多个pdb文件，是否可以使用rms frame mass？

Yeah that command can give you and average structure from a number of frames, for align multiple pdb I think you can make a script using cpptraj or a python script using mdanalysis

molly85

rpestana94 发表于 2023-12-26 00:06
Yeah that command can give you and average structure from a number of frames, for align multiple p ...

好的，谢谢老师！