Hi,
I am looking to add [Fe4S4]+2 parameters to the charmm36 forcefield file but am kinda lost. Has anyone attempted to do this. P.S. got the parameters from QM data.
Parameters for these species were published years ago by Toshiko Ichiye’s group. The patching process is complicated in CHARMM, and involves modification of Cys side chains. It may be difficult or even impossible to get this to work in GROMACS given that you need to make a set of simultaneous, non-linear bonds in the polypeptide chain. It may be possible via specbond.dat but would likely be very challenging. Adding such a cofactor requires four simultaneous modifications.
It has been implemented in a more recent study by de Silva et al. (2022) (DOI: 10.1080/07391102.2020.1847687) in GROMACS v2019