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?
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.
I am facing same problem with my mol2 file ( [Hypervalent carbon (valence=5) not supported CGenFF]). Mr jalemkul can you please elaborate on how to fix the chemistry before running through CGenFF server?
Any carbon atom may only participate in 4 bonds. Your
.mol2 specifies 5 via a combination of single bonds, aromatic bonds, etc. listed in the BONDS heading. You need to identify which atom is the problem and correct the bonded structure.