Unable to generate topology with graphene about ligpargen

[therealchrisneale]

Your PDB file is incorrect due to spacing issues. Some noted below, but also the entire PDB format depends on certain columns so you might get better results if you have proper PDB format for your input. Also, unless it is a sphere, don't you need to add at least some hydrogens?

...
HETATM 7 C7 GRA 7 53.198 -1.401 0.100 1.00 0.00 C
HETATM 8 C8 GRA 8 53.116 -0.901 -2.303 1.00 0.00 C
HETATM 9 C9 GRA 9 53.034 -0.400 -4.706 1.00 0.00 C
HETATM 10 C10 GRA 10 53.525 -0.573 6.537 1.00 0.00 C <-- change in spacing
...
HETATM 22 C22 GRA 22 53.279 3.759 -3.848 1.00 0.00 C
HETATM 23 C23 GRA 23 53.198 4.260 -6.252 1.00 0.00 C
HETATM 24 C24 GRA 24 53.116 4.760 -8.655 1.00 0.00 C <-- change in spacing
HETATM 25 C25 GRA 25 53.853 3.086 9.798 1.00 0.00 C
HETATM 26 C26 GRA 26 53.771 3.586 7.394 1.00 0.00 C

[layzhaf]

Dear Prof/Dr

Thanks for the comments. I would like to investigate the electrode double layer of graphene. So supposedly no H should been attached to my double layer nanosheet unless for water ions.