GROMACS version: 2019.4
GROMACS modification: Yes
Dear gromacs users,
I’ve try to use Parmed to convert gromacs topology file into amber prmtop file format.
But in the my python script
gro_top = pmd.load_file('topol.top') line, error occured below:
parmed.exceptions.MoleculeError: Cannot bond two virtual sites/extra points together
Because the topology file didn’t have any problem when I run MD simulation, I don’t know why the topology file raised error.
I make the topology file that I attached by using pdb2gmx with the GROMOS54a7 force field.
topol.top (674.9 KB)
Could you tell me what I’m missing?