Hypervalent carbon (valence=5) not supported CGenFF

User discussions
1

Dear Gromacs Users,

I would like to perform MD simulations of protein with ligand molecule. Now I am preparing ligand parameter using CGenFF similar with Gromacs Tutorial #5. However, CgenFF gives an error as following:
Hypervalent carbon (valence=5) not supported CGenFF.

If you have any experience, please let me suggest other possibility to prepare parameter of ligand molecules?

Best regards,

Mijiddorj

2

Carbon can’t form 5 bonds, but your .mol2 file assigns at least one C atom 5 bonded neighbors. Generate a proper .mol2 file with correct chemistry before trying to run CGenFF.