Cpptraj: RMSD as a function of Residue Number?

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Aditya Kumar Sarkar

AMBER tools have an utility called cpptraj. This utility can calculate "Per residue RMSD". You can go through the Manual of AmberTools15 or any of its version but not less than 12, in the chapter "cpptraj" you will get the "rmsd" option and details of how to calculate "Per res RMSD".

To get an average for each residue, you can use R. Getting average is pretty simple.

Hope this help.