[gmx-users] Does Gromacs work on a molecule which is not protein

[Tanping Li]

Dear all,

I plan to run solvate a small molecule using Gromacs.
This small molecule is not a protein or DNA or RNA. So
I meet the problem at the first step to run pdb2gmx,
the wrong information says Gromacs can't recognize
this molecule.
Is there a way to assign charge to this small molecule
and get a *.top file; could I use gromacs to run this
unknown small molecule?

Thank you very much for your suggestion. I have
bothered by this for a while.


Best
Tanping