Sir,
In the case of a DNA ligand system, at the start the counterions were
somewhat uniformly arranged around the complex to give a neutral system.
Now during the production run (usualy without any restraints) the
counterions(Na+) move away from the DNAligand system to a side so that they
are now not around the complex but near to one side opposite to the binding
region. The system (the binding) is not stable. I would like to know, may
be this state of the counterions have some contribution to the observed
instabilty.
Thanking you
On Tue, Jun 11, 2013 at 2:12 PM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Dear Mary,
>
> This is a very open question and not a very clear one.
> I presume you are talking about a system with two solute components that
> interact (bind), i.e. two proteins or a protein and a ligand, for example?
> And what exactly do you mean by 'binding stability'?
> The simple answer would be 'yes', as any starting condition, such as the
> starting coordinates of ions, will cause a difference in the MD trajectory
> obtained. And unless you look at properties that will be thoroughly sampled
> in the time of your simulation (which are few properties of typical
> interest, and almost certainly not the possible conformational sampling of
> two solutes with respect to each other), you will get different answers
> from different MD trajectories.
> Maybe this helps...
>
> If your question is more about a specific issue, then please rephrase it
> accordingly.
>
> --Marc
>
> On 11 June 2013 09:27, Mary Varughese <maryvj1985.gmail.com> wrote:
>
> > Sir,
> >
> > does the spatial arrangement of counterions around a complex affect the
> > binding stability of the system during the production dynamics.
> >
> > Thanking you
> >
> > Mary Varughese
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Received on Tue Jun 11 2013 - 02:30:02 PDT
