I have written a C++ program that can do it for you in 5 minutes. If you interested I can send you link to executable.
It counts #of solute molecules and #Na+ and Cl- ions plus DMPC, but I can adjust it so it can count any number of molecules, I need to know how many atoms per molecule and it reads gro file now, I do not work with pdb, but if needed I can do it form pdb too.
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