GROMACS version: 2020.3
GROMACS modification: No
I have two forcefield .itp files. One is given by CHARMGUI membrane builder FF converter from modelling an asymmetric membrane of LPS/POPC. The other is generated from pdb2gmx when I initialised my protein from a pdb file. I am adding my proteins above the membrane, however there is inconsistencies between the forcefields. Using one or the other, some atoms cannot be found. for example Atomtype NH3 not found in my peptide or atomtype HCA2 not found in my LPS molecule. How can I get round this to simulate my system successfully? Both systems simulate successfully on their own!
You can adapt and follow steps 3-5 from this Gromologist tutorial:
If the two topologies are built with identical FFs, and the only thing missing are the atomtypes and bonded parameters, you can skip the prefix_type keyword - it effectively adds a prefix to all atomtypes in one of the topologies to make sure there are no conflicts in parameter values, which is the “safe” option.