[gmx-users] modeling of zwitter-ions

[Olga Selyutina]

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?
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?

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Best regards, Olga Selyutina