Dear AMBER users,
I am simulating a G quadruplex system which
requires the presence of alkali metal ions and water molecules for
stabilizing the tetrad core. What I am really interested is in exploring
the energy landscape of the system. So I cannot include too many water
molecules explicitly as I am limited by computer power. I tried simulating
the system with an implicit solvent (igb = 1) but the potassium ions in the
channel are expelled during minimization. I cannot do away with the
potassium ions and include salt effects in an implicit manner as the
stacking of the guanines in the core would get affected. What I intend to
do is to create a layer of water molecules around the GQ (solvateshell) and
model the solvent outside the layer implicitly. I looked through the
archives, but could not find much. I would like to know whether it is
possible to implement this in AMBER9 . I would also be grateful if someone
could critically comment on this.
Best Regards,
Debayan Chakraborty,
PhD Student,
University of Cambridge
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Received on Thu Jan 31 2013 - 20:00:02 PST
