Error when the Parmed package read the gromacs topology file

User discussions
1

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?
Thank you

2

This is an issue with ParmEd and you should contact its authors. Your topology apparently has some setup that their conversion scripts can’t handle.

3

Thank you :)