I am beginner in MD simulations, and I am struggling with understanding how to parameterize a molecule which is not available in the forcefield, such as HEME or iron-sulfur clusters for example.
I would appreciate if some one helped me by showing me the exact steps for doing this.
this is a kind reminder
Don’t try to parametrize them yourself; parameters already exist for heme and Fe-S clusters in most force fields, though they aren’t implemented in GROMACS. You will have to add them yourself by following http://manual.gromacs.org/current/how-to/topology.html#adding-a-new-residue
Fe-S clusters will also require modification of
There are several examples of different groups developing this parameters and implementing them, e.g. https://pubs.acs.org/doi/abs/10.1021/ct300185u and others (easily found via Google search), so you should contact the corresponding authors of any such papers and ask for example inputs or topologies.
Thanks a lot Jamelkul for your reply.
One last question. in case if I need to perform MD simulation with an implicit solvent model so I need the gbsa parameters for those new defined atomtypes. so how could calculate them ? or form where could I get them ?
Just like any other element of a force field, these quantities are parametrized against some target data. I do not know the source of the GBSA parameters in GROMACS but note that the implicit solvent features were removed in more recent versions due to lack of use, lack of development, and general opinion that such simulations are fairly inaccurate.
Thanks a lot Jalemkul.