> At the moment I am fighting with a problem, which I expected to be
> trivial. I would like to use an ammonium ion (NH4+) in a simulation of a
> protein-ligand complex. To make things easy, I just used antechamber for
> the parameterization. The resulting charges look pretty reasonable.
> However, when minimizing the system, the ammonium ion gets completely
> deformed with all protons on one side of the nitrogen atom in an almost
> perfect square. The binding site is very polar and I am wondering if
> this could be causing the problem.
>
> Is there any possible way to keep the tetrahedral conformation without
> strongly constraining it?
