On Mon, Jan 28, 2013 at 9:04 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 ?
>
I would suggest against using GB for nucleic acid simulations. igb=1 has
shown stable dynamics for NAs in the past, I think, but I think the general
consensus is that you need explicit solvent generally. I would argue this
is _especially_ true if you have structural ions.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jan 28 2013 - 08:00:02 PST
