MD simulations with nucleic acids
Hi! I normally work with systems limited to proteins and small molecules, but recently I was reached out for collaboration that focuses on studying interactions between proteins and nucleic acids. I already got my simulation plan ready, but I was wondering if there are any special caveats I should keep in mind when working with such systems. It sounds pretty straightforward to me since the majority of the FFs already include parameters for nucleic acids, but recently I discovered, for instance, that zinc-oriented proteins are not represented correctly by CHARMM36 due to zinc ion recruiting two water molecules leading to disruption of zinc-oriented shell and if I wanted to simulate such system I would have to use special force fields like (E)ZAFF or use distancs restraints/dummy molecules. I was wondering if there are any special considerations of this kind when it comes to MD simulations involving nucleic acids as well. For context, I plan to use CHARMM36 ported for GROMACS, but I am ready to adjust (not sure about learning new software, though). Thank you in advance!