[gmx-users] Gromacs tools mistakenly change the name of atoms incoordinate files

[chenmengen]

You should always use the "gro file" generated by pdb2gmx or the "equal" pdb file (same topology and nomenclature but different format). Because not only the nomenclature could be deferent between your original pdb file and the top file, but also the number and indexing of atoms may also be deferent. I think the waring is aware you that it's encountered topology mismatch.