Dear gromacs users, I am working on a membrane protein ligand binding simulation. I have generated a solvated membrane-protein system using charmm-gui and added 150 mM KCl counterions and separately parametrized the ligand. Later inserted the ligand molecule manually using gmx insert replacing some of the water molecules. SInce the ligand was charged, I added 6 more Cl- ions to neturalize the system at the end.
I already have the topology file and the corresponding protein, lipid, ions and water topology (itp) and forcefield.itp files where all the atomtypes and the [ defaults ] section defining the combination rule and non-bonding interaction parameters are already defined. When I parametrized the ligand separately on charmm-gui, it also generated a ligand forcefield file: lig_forcefield.itp (much like the forcefield.itp file containing all atomtypes and non-bonding and bonding parameters etc.) and a ligand.itp file describing all charge, atoms, bond, angle, dihedral connectivity etc.
Now when I included the ligand forcefield file (lig_forcefield.itp) directly in the topol.top file right after the inclusion line of the original forcefield.itp (containing only protein+lipid+water+ion) gromacs was showing an error about “duplicate entry for [ defaults ] section”, so I commented the [ defaults ] section and its entries (i.e. comb-rule, nonbonded function, gen-pair etc.) in the lig_forcefield.itp file as the those details regarding the [ defaults ] directive (comb-rule, non-bonded interaction function) are already defined once in the forcefield.itp file (for the protein+membrane+water+ions).
Now when I commented the two lines referring to the [ defaults ] directive in the lig_forcefield.itp file, grompp is working fine and I am not having any errors.
Is this the correct way of incorporating the ligand parameters? or also I can simply copy the [ atomtypes ], [ bondtypes ], [ dihedraltypes ], [ angletypes ] and the [ pairtypes ] directives and their entries from the ligand-forcefield.itp and copy that to the forcefield.itp (originally obtained in absence of ligand) and then work.
I AM CURRENTLY WORKING ON A PROTEIN-LIGAND SYSTEM LIKE THIS, ANY HELP OR SUGGESTION WILL BE MUCH APPRECIATED, THANK YOU.