Justin asked "Is this the only output? What is the whole output of
the command?"
And while you did post the entire output, one might notice that the
actual warning has nothing to do with protein/non-protein.
WARNING 1 [file aminoacids.dat, line 1]:
T-Coupling group azoct has fewer than 10% of the atoms (33 out of 3660)
Therefore, no, you should not ignore this warning. Change your
temperature coupling groups to something more reasonable. Generally,
that would mean join the smallest group with one that makes sense.
Sure, 10% is an arbitrary selection, but there is a lot to be careful
about here.
http://wiki.gromacs.org/index.php/Errors#T-Coupling_group_XXX_has_fewer_than_10.25_of_the_atoms
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