You may find the ions are expelled even during explicit simulations. Ions
are generally not modelled well by fixed charge MD. I would recommend
building modified residue force fields for the liganding residues such that
the potassium is covalently bound
On Jan 28, 2013 9:05 AM, "Debayan Chakraborty" <debayan.ch.gmail.com> wrote:
> Dear AMBER users,
> From the AMBER archives I gather that
> implicit solvent simulations using models such as GB with explicit ions are
> not recommended, but I am trying to simulate a G quadruplex which requires
> potassium ions to hold the stacks together (in fact I tried simulations
> with GB and salt effects taken implicitly but they did not give the correct
> stacking ). The potassium ions that were initially placed in the core of
> the quadruplex were expelled during the simulations with GB. Has anyone
> experienced the same problems, and give suggestions as to what could
> possibly be done to circumvent this ?
>
> Best Regards,
> Debayan Chakraborty,
> PhD student,
> University of Cambridge
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Received on Mon Jan 28 2013 - 07:30:03 PST
