GROMACS version: 2016
GROMACS modification: No
I am beginner in MD simulations, so please excuse my basic question.
I am trying to work on proteins which mostly has non-protein molecules and ions such as (Hg, Zn or SO4 and so on ). I need to optimize those proteins using the implicit solvent model.
it seems that gromacs has no GBSA parameters defined for those ions and molecules. so my question is how to compute those parameters for new atoms and ions ?
Thanks a lot