My systems contains proteins + Nucleic Acids + Mg2+ ions. First I solvate this using gmx solvate and then I try to neutralize the system using gmx genion with the option "-neutral". However, I see that sufficient no. of Na+ ions are not added. Please let me know if anyone has any idea. If needed I can share my initial pdb files.
After the gmx grompp command, in the terminal window, see if the charge of your system is negative or positive, based on that add equal no (X) -nname CL -nn X (if charge is positive) or -pname NA -np X (if charge is negative) ions.
Hope this fixes your problem.
regards
Tanuj
Yes, I did that. it was showing -X charge so I added "-name NA np +X". This definitely sorted my problem but I wanted to know why -neutral did not work correctly. And if anyone else has experienced this issue?
I have encountered the same issue, and I don't understand why? From my experience, you have to define the charge of the MG using the option pq.... -pname MG -pq 2
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