GROMACS

gmx solvate (as per its documentation) can update the topology file to include the number of solvent molecules under the [ molecules ] caption. Typically, this is the last caption of the topology file, so appending new lines is straightforward. However, if other captions (namely [ intermolecular_interactions ]) after [ molecules ], then the "SOL <nmol>" line appears at an incorrect place.

gmx genion works the same way, only it removes all lines from under [ molecules ], including 'Protein' and 'SOL' and place them at the end of the file.

My current workaround is not to use the topology updating mechanisms of these two tools but edit the files by hand or do patching in scripts.

I have tested this with gmx 2019.1, but I think older versions might also be affected.

Thank you for your help!