I'm trying to compare the loop6 motion in TIM (PDB: 2jk2, open .xtc file) with the crystal structure of loop 6 in the closed state (PDB: 1hti, em.tpr file) using an rmsd analysis in Gromacs. Unfortunately, both structures have different atom numbers, resulting in the following fatal error:

"Molecule in topology has atom numbers below and above natoms (7435).

You are probably trying to use a trajectory which does not match the first

7435 atoms of the run input file.

You can make a matching run input file with gmx convert-tpr"

I tried making an index file out of the crystal structure to only include the residues found in the xtc file, but I only get 7431 atoms. Can someone help me and explain what I did wrong, and what i should have done?