Superimposed PCA for two proteins, mutated (with deletion) and wt

GROMACS version: 2021.4
GROMACS modification: No

Hello everyone,

I have two trajectories: one is a wt protein and his mutated version with a deletion of an amino acid.

My aim here is to plot the two PCAs superimposed, to see if the space that they explore matches. Nevertheless, I can not superimpose directly the two PCAs (they have different components, non comparable).
On this very blog, I found another guy asking for help and he ended up using

gmx anaeig -s WT_md.gro -f WT_md.xtc -v WT_eigenvectors.trr -first 1 -last 2 -2d WT_2d.xvg
gmx anaeig -s WT_md.gro -f MUT_md.xtc -v WT_eigenvectors.trr -first 1 -last 2 -2d MUT_2d.xvg

However, in my case this does not work because the eigenvectors calculated fro the WT include the amino acid that is missing in the second structure, therefore GROMACS can not create a match between the components and the mutated version of the protein (“you selected a group with 193 elements instead of 194, your selection does not fit the reference structure in the eigenvector file.”)

I used the C-alpha selection to generate the eigenvectors. I do not find an alternative that would solve my problem.
Can someone help me?