Using VMD I made two layers of graphen and then I filled between the two sheets with a water box, but VMD does not have NH4+ and OH- ions to ionize my water box. I tried to use chimera but I couldn't find these two ions in the chimera's ion list. I think CHARMM also does not have Param and Top files for NH4+ ( I think you can produce them but it is not straightforward). I tried to check Charmmgui, but it gave an error regarding my PDB that is made in VMD and some other issues, so I couldn't reach that point to check if it can include these ions. Can someone please help me to find the easiest way to overcome this problem?
Now that from VMD output I know how many water molecules I need by having the pdb file for these ions, can I use Packmole to make the water box and include these ions and then concatenate them to the pdb file of the two layers of graphene?
any advice would be greatly appreciated
For those who may have the same question in the future,
I used OpenBabel to generate the PDB file of the desired ions and then used packmol to make the water box and ions. If packmole gives an error due to your PDB format you can convert it into vmd format.
http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
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