RMSD filter

Hello:

I have been working with the RMSD filter to calculate the similarity between different coronavirus spikes. One error I got on some comparisons was that the position of the requested sequence was greater than the amount of residues in the pose. When reviewing the structures in PyMOL I could see that the numbering of the residues is not consecutive, that is, it starts at 1 for chain A, it continues normally and when starting chain B it starts at 1 again, that is, it never ends in the same residue number than in the alignment I provide. I know that rosetta has its own residue numbering on poses, but could this be the problem? Thanks in advance.