You can do PCA on Desmond trajectory in VMD using prody (http://prody.csb.pitt.edu/tutorials/nmwiz_tutorial/pca.html).

Prateek Kumar

This should be the easiest tutorial http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA

Check it.

You need to convert the trajectory to series of PDB files and you can use https://github.com/charlesdavid/JED for PCA analysis

Thank you for all valuable suggestions.

Pytraj PCA

https://amber-md.github.io/pytraj/latest/tutorials/tutorial_pca.html