[gmx-users] No such moleculetype ZN

elham tazikeh elham.tazikeh at gmail.com
Wed Jun 4 20:25:16 CEST 2014

Dear Justin

Please ignore my previous questions.

I want to do 2 md simulations: 1) protein and Cu, 2) protein and Zn.
After checking

force fields in gromacs 4.5.3, I found oplsaa in which there are both
Cu and Zn ions

in atomtype.atp file. Then I used gromacs 4.6.5 (with opls force
field) to do md

simulations. I added ions to my system using genion command.

genion -s ions.tpr -o sol_ions.gro -p topol.top -pname CU -pq +2
-neutral -conc 0.025.

genion -s ions.tpr -o sol_ions.gro -p topol.top -pname ZN -pq +2
-neutral -conc 0.025.

In both cases, ions were added without problem. Then, I used

grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr

In case of protein and Cu, there is not problem. But, in case of protein
and Zn,

I encountered error: No such moleculetype ZN.

I checked ions.itp in opls force field in gromacs 4.6.5, I found, there are both

Cu and Zn ions in atomtype.atp file. But, there is only Cu in ions.itp file.

How to do md simulation of protein-zn system using gromacs 4.6.5.

Any help will highly appreciated.

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