[gmx-users] No such moleculetype ZN

Mark Abraham mark.j.abraham at gmail.com
Wed Jun 4 14:07:32 CEST 2014


It's hard to understand what you're doing, but take care to distinguish
atom name, residue name, and moleculetype name, which can all be different
depending on the GROMACS version and force field.


On Wed, Jun 4, 2014 at 10:50 AM, elham tazikeh <elham.tazikeh at gmail.com>

> Dear Justin/ *Dhanachandra *
> *thanks for your reply*
> *as you konw, i simulated Zinc cation on hGH protein*
> *and received  an error in energy minimization  process in em.tpr
> production(*grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr)*, as
> below:*
> *No such moleculetype ZN*
> *in one hand, i checked my ions.itp file and saw there is no ZN ion in it,
> but atp file in my choosed force field (opls) support ZN ion same CU ion
> (about CU cation, i had not any problem)*
> *on the other hand, by genion command, i could replace ZN ions instead of
> sol (water) molecules, easily*
> *i don,t know it,s related to my version pf gromacs 4.6.5 or not?*
> *Regards*
> *elham tazikeh*
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