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 second simulation: 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
