GROMACS version: 5.1.1
GROMACS modification: No
Dear Gromacs users,
I am trying to do an MD simulation of a peptide(with synthetic amino acid and aliphatic linker) and mRNA. OPLS and amber14sb_OL15 force fields are selected to model peptide and mRNA respectively. When I perform the ion addition step (group command), I received the following error.
Can anyone suggest to me how to solve this issue?
There’s your problem. You cannot mix different force fields for different parts of the system. You need to choose a single, self-consistent force field. The error you’re getting is because your topology contains two different force fields, which define separate sets of atom types.
Thank you @jalemkul , I tried to find a force field for my system. However, I couldn’t find any force field which can use for both peptide and RNA . Can you propose me any force field ?
Both CHARMM and AMBER can handle these types of systems. The AMBER force fields in GROMACS are wildly outdated, though, and you will need to obtain an updated force field from some external source. Note that AMBER is developed in a way such that their overall force field is internally self-consistent, but they will refer to protein and nucleic acid parameter sets by very different names (e.g. ff19SB for a recent protein parameter set, OL15 or parmbsc1 for nucleic acids). But they can be used together as they are all still AMBER.
CHARMM is just CHARMM :)