[gmx-users] Vacuum Simulation

[Joanne Hanna]

Hi

I am trying to simulate my system in vacuum, i have run my protein and one of my ligands (a single phenylalanine) through pdb2gmx and selected the correct forcefield, however i am unsure of how to treat the charges for my other ligand AMP(2-) and the ion present Mg(2+). is it sufficient to allow these to balance each other out, or should each individual molecule carry a zero charge.

Many thanks
Jo

Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL

J.F.Hanna at warwick.ac.uk
jfhanna at gmail.com