Protonation states using -inter

User discussions
1

GROMACS version: 2020.4
GROMACS modification: no

If I want my protein residues to be in the default protonation states in physiological pH, for example, Lysine +1, Glutamine (0), Glutamic acid (-1), and so on … should I skip the -inter flag at the beginning while doing pdb2gmx? and just generate the topology files while letting gromacs decide the charges?
or is the protonation assignment something that should be done, otherwise there might be some problem assigning the charges.

2

pdb2gmx automatically assigns protonation states assuming canonical pKa values and a pH of 7, so you don’t need to do anything via -inter if you just want all the conventional protonation states of titratable residues.