[gmx-users] genion

Justin Lemkul jalemkul at vt.edu
Sun Mar 16 15:03:59 CET 2014

On 3/16/14, 9:49 AM, Andrew Bostick wrote:
> Dear Kalyan
> Thanks for your reply
> I want to use Zn2+ ions with my protein.
> There is Zn2+ ions in atomtypes.atp file of opls force field. But there is
> not Zn2+ ions in ions.itp file of of opls force field.
> Based on your answer, now, I can not use Zn2+ ions in genion tool.
> Is it true? But I used
> genion -s ions.tpr -o mol.gro -p topol.top -np 2 -pname ZN -pq +2
> and I did not encountered with error and solvent molecules replaced with
> Zn2+ ions.
> I confused. Please give me more explanations.

genion does not read ions.itp to understand which ions it can and can't add.  It 
does what you tell it.  You can name your monovalent ions anything you like at 
this stage; the only thing that matters is that the name supplied corresponds to 
some known [moleculetype] in that force field - either in ions.itp or in an .itp 
file of your own creation.  If there is no ZN [moleculetype] anywhere, grompp 
will die with a fatal error.



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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