[gmx-users] modeling of zwitter-ions

[Justin Lemkul]

On 2/5/20 9:16 PM, Olga Selyutina wrote:
> Hello,
> I'm simulating a molecule which is aminoacid connected with drug throuch a
> "bridge" of a few C-C bonds. Molecule should be in zwitter-ionic form,
> where negative and positive charges are distributed in pi-systems of drug
> and amino-acid, accordingly. Which is the best way to build the topology of
> such zwitter-ion?

You'll have to parametrize it yourself. Aromatic groups in amino acids 
don't carry net charge.

> And one more question. The solvent is acetonitrile and it's important to
> take into account the solvation effects in this system. I'm working in
> gromos54a7 forcefield. Which acenotitrile model is better for solvatation
> effects?
>

You need a solvent model that has been parametrized in a manner 
consistent with the protein force field.

-Justin

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Justin A. Lemkul, Ph.D.
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