[gmx-users] No such moleculetype ZN

[Justin Lemkul]

On 6/4/14, 2:25 PM, elham tazikeh wrote:
> 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.
>

It may not be possible, but that's a force field issue, not a software issue. 
Most force fields don't cover more than a few metal ions, and even then the 
parameters for transition metals are generally incapable of capturing the true 
physical behavior of these ions.  Such is the limitation of additive MM force 
fields.

The Zn parameters were indeed removed from OPLS; their parameters were either 
undocumented or found to be incorrect.  So it is possible to use 4.5.3 to "make 
things work," but the parameters you're applying are not trustworthy.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================