Hi,
Well, I would say it is best to do without restraints. It is likely you
won't need them; if the ATP phosphate groups stay reasonably in place, then
the electrostatic interactions between Mg2+ and the negative partial
charges of the phosphate oxygens will keep them together.
But it is important to monitor what happens in the simulation.
Also, consider the Mg2+ parameters you want to use; you may want to
consider the more recent Mg2+ VdW parameters from Allner et al. (see below).
If you find the Mg2+ doesn't stay in place (even with the updated
parameters), you could consider distance restraints, but this is certainly
not ideal.
Good luck,
Marc
Olof Allnér, Lennart Nilsson, and Alessandra Villa
*J. Chem. Theory Comput.* *2012* 8:1493-1502
*Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations*
On 2 December 2014 at 19:59, BERGY <nucleic81.gmail.com> wrote:
> Hi amber -users,
>
> I have a protein crystal structure with ATP in the ligand site and a
> coordination bond with 6 oxygen atoms. i.e. three from water oygen, OH
> from Serine, two oxygens from ATP. They all are within 2.1 Angstroms from
> the Ion. The question is, while carrying out the simulation, Is it
> necessary to have some distance or angle or dihedral restraints to maintain
> the coordination bonds.
>
> Best,
> Bergy
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Received on Tue Dec 02 2014 - 13:00:02 PST
