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
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.
I have identified the problematic carbon. Could you tell how can I correct the bonded structure?
I have attached the mol2 file in txt format (I have copied the contents onto a txt file cus the site does not allow me to upload .mol2 or .zip file) for your reference. The problematic hypervalent carbon is C17.
Thank you.
LIG.txt (5.5 KB)
The sum of the valence of all bonds to that carbon must be 4. Aromatic (ar) are 1.5, single is 1, double is 2.