On Wed, Mar 16, 2022, liu kai wrote:
> After few ns production run, I found two Na+ ions close (about 2.5 Angstrom)
> to the phosphate group, except the Mg2+.
Can be elaborate here? Do you mean that the Mg2+ left the vicinity of the
ATP? Or do you mean that the Na+ ions came close to the phosphate oxygens,
but not close to the Mg2+?
> I think the Na+ should not be close to the phosphate group.
> If the simulation is correct, does it mean that ATP can coordinate with
> two Mg2+ ions at the same time?
A single Mg2+ only neutralizes part of the -4 charge of ATP. So other
cations are certain to come close during MD. Why to you think that Na+ ions
should not come close? The origin of your question about two Mg2+ ions is
not clear to me: did you see this sort of behavior in your simulation?
The Buelens et al. paper you cite is a good starting point here. Carlos'
questions about what ion and water models you are using are also good
points. Commenting on the relative concentrations of monovalent and
divalent ions would also help.
....good luck....dac
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Received on Wed Mar 16 2022 - 11:00:02 PDT
