GROMACS version: 2022.5
GROMACS modification: Yes
I have modified gromacs amber99sb-ildn force field for zinc parameterization. It has extra ASZ and GLZ residue and also modification for Zinc binding oxygen as OZ. With this new force field grompp command for ionizing the solvation box is not working. Giving error “invalid bond type 0”. What should I do now ?
You need to add parametrization for these atomtypes in ffbonded.itp and ffnonbonded.itp files in your ff directory. In ffbonded.itp there are several sections for different types of forcefield coefficients : bond, angle, dihedral etc. You need to add proper type and value of coefficient in every section of ffbonded.itp for each combination of these new atom types in your residues. I suppose it can be just repeating of all lines suitable for GLU and ASP residues with substitution of corresponding atoms.
Dont forget to add new residues to residuetyes.dat and aminoacids.hdb