CHARMM36 or AMBER parameters for H+ ion

User discussions
1

GROMACS version: 2023.2
GROMACS modification: No
I would like to model H+ ion for my simulations but couldn’t find parameters for it. I understand that pH-dependent changes are studied by modification of protonation states of proteins. Even hydronium ion has been parameterized but not H+ ion. Can anyone please point to any relevant reference or FF parameters of H+.

Thanks,

Raman

2

H+ doesn’t exist in aqueous solution, hence why H3O+ has been parametrized but H+ hasn’t. If you want to look at pH-dependent changes in dynamics, you need constant-pH simulations or different fixed-protonation simulations. But there, you would not have any kind of protons floating around, you would be looking at different protonation states of the relevant chemical groups.

3

Thanks Dr. Lemkul for your reply and clarifications.

This was really helpful.

Regards,

Raman