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