[gmx-users] No such moleculetype ZN

Justin Lemkul jalemkul at vt.edu
Wed Jun 4 14:16:35 CEST 2014

On 6/4/14, 4:50 AM, elham tazikeh wrote:
> 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?*

If the force field has parameters for ZN, then simply add the appropriate 
[moleculetype] to ions.itp.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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