[gmx-users] How to introduce Mg2+ ions to system that are necessary for nucleotide co-enzymes?

Justin Lemkul jalemkul at vt.edu
Tue Jan 6 14:46:10 CET 2015

On 1/6/15 8:25 AM, Hassan Aaryapour wrote:
> Dear Gromacs Users
> I want to do an unguided molecular dynamics simulations (500ns) with GTP or
> GDP ligands that place at a random location within a simulation box that
> also contained my kinase protein. How can I add or introduce Mg2+ ions to
> system that are necessary for GTP or GDP ligands? How much Mg2+ is required
> for GTP or GDP molecules in a cubic box with -d 1.0???

So you're hoping to observe unbiased binding of GTP/GDP and Mg2+ to the enzyme 
active/binding site?  If that's the case, then the binding stoichiometry tells 
you how many of each species you need.

> Is it logical I add ions to a system with -8.99999 net charge using command
> below?
> # gmx genion -s ions.tpr -o conf-ion.pdb -p topol.top -pname MG –np 4
> -pname NA -np 1 -nname CL

No, this is an invalid command since you have multiple -pname (which you will 
see if you actually run the command...)  Add the number of Mg2+ that you need 
(see above), then neutralize and/or add some relevant concentration of NaCl in a 
second step.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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