GROMACS version:2023.2
GROMACS modification: Yes
I am simulating HDAC11 protein with its known inhibitor FT895 in GROMACS 2023.2. As HDAC11 has zinc, I modified the forcefield in amber-ildn described in the paper https://doi.org/10.1021/acsomega.0c01337. But after modifying the forcefield, I can not ionize the solvated box with the command “gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr”. It produces an error “Invalid bond type 0”. Can you please help me with that ? For convenience i am uploading ions.mdp file and modified forcefield file.
ions.mdp (1021 Bytes)
It seems like the forcefield modifications you made were not correct. Go through all your modifications and verify that they are correct. Start with the bond types that you have changed or added.