[gmx-users] charged & uncharged ligand
shahab.shariati at gmail.com
Tue Aug 5 13:01:04 CEST 2014
Dear gromacs users.
My system contains protein + ligand.
Total charge of my protein = 0
My ligand has -NH2 group.
I want to do 2 md simulations:
1)deprotonated state of ligand (-NH2). => Total charge of system= 0
2)protonated state of ligand and (-NH3+)=> Total charge of system=+1
I have no problem about the first simulation. I have a question about the
Should I one Cl ion to system using genion tool? I want to study effect of
the charged ligand on the protein.
Any help will highly appreciated.
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