What are the steps needed to find the PCA of protein-ligand complex?

GROMACS version:2020.1
GROMACS modification: Yes/No
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hello all,
have a 100ns sim .xtc file for a protein ligand complex. for the calculation of the pca i first center the complex applied rotational and translational fitting gmx trjconv and then went into the steps of gmx covar and gmx anaeig.

the problem is when i see the -extr structure the ligand is getting distorted so much that I can’t figure it out where is the error.

Can someone please help me out where I’am getting wrong? I’m new to gromacs.

steps i followed:

echo 22 22|gmx trjconv -s md_01.tpr -f 100ns_sim.xtc -o md_0_100_center.xtc -center -pbc mol -ur compact -n index

echo 22|gmx trjconv -s md_01.tpr -f md_0_100_center.xtc -o nojump.xtc -pbc nojump -dt 100 -n index

#echo 22 22|gmx trjconv -s md_01.tpr -f md_0_100_center.xtc -o md_0_10_fit.xtc -fit rot+trans -n index

echo 22 22|gmx covar -s md_01.tpr -f md_0_10_fit.xtc -o eigenvalues.xvg -v eigenvectors.trr -xpma covar.xpm -n index

echo 22 22|gmx anaeig -s md_01.tpr -f md_0_10_fit.xtc -v eigenvectors.trr -eig eigenvalues.xvg -proj proj-ev1.xvg -extr ev1.pdb -rmsf rmsf-ev1.xvg -first 1 -last 1 -nframes 90 -n index.

22 is protein_ligand .

#- i removed this and checked whether same thing is happening or not. I’m attaching a screenshot of the -extr structure i got. can someone help how we get non distorted structure of the ligand here??