A shift in molecules between topol.top and solv.gro

I have spent literally days and days trying to match atoms in topol.top file with solv.gro there is always 1 or 2 two atoms more or less that shifts the matching of the two files.

I ran the same commands on the 3HTB tutorial on GROMACS website and it works but using my dimer protein the two files would never match…

I gave up.

You will need to provide more specific details about the problem (exact commands, exact terminal outputs, etc) to get any kind of useful help. You should never have to make manual edits to files.