How can I confirm the protein was protonated with pdb2gmx commands. It will be protonated at ph that I need to run simulation with it (ex 2.4).
pdb2gmx adds hydrogens according to *rtp file in $GMXLIB folder. you can choose your own charge using flags -arg, -asp, -glu etc. (check pdb2gmx -h), but you must know what charge is appropriate to your desired pH.
One way to know the protonation state of your protein in a defined enviroment is using the H++ server, that gives you a new pdb protonated. The problem is GROMACS does not keep this protonation state when you make pdb2gmx, but you can use the information from H++ to protonate manually your protein with pdb2gmx, using flags as Michal says. To check just go to the .gro file and see if the resid has or not the protons you want.
I'm not sure if I understand your question correctly, because the previous answers tend to a different direction.
But if you simply want to know if pdb2gmx protonated or deprotonated a certain polar sidechain (which would happen at a given pH value and this is how I interpret your question), you can simply look at the output file (e.g. using VMD, this can also open .gro files) and check if there are hydrogen atoms added or removed at the given position.
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