CPPTRAJ command to measure distance between two regions

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#here the command measures the distance between two loops (considering the c-alpha atoms in the loop) and prints output in L1-L2.dat.


For amber MD trajectory you may try using the following commands in CPPTRAJ:


$AMBERHOME/bin/cpptraj

>parm pro_solv.prmtop

>trajin md-autoimage.nc

>rmsd pro @CA,C,O,N,H first mass

>distance :135-149@CA :156-166@CA out L1-L2.dat

>run


Reference: Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1.

https://doi.org/10.1021/acs.jcim.0c01080

https://www.researchgate.net/publication/348511593_Interplay_among_Structural_Stability_Plasticity_and_Energetics_Determined_by_Conformational_Attuning_of_Flexible_Loops_in_PD-1


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