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 - 06:30:02 PST
