On Fri, Feb 01, 2013, Debayan Chakraborty wrote:
> 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.
Are you sure that you cannot afford straightforward explicit solvent
calculations in a periodic box? Because of the efficiencies of the PME
method, these are often faster than GB calculations, especially for larger
systems.
Amber does not have a good implementation of mixed explicit/implicit solvent
models (e.g. with a shell of explcit waters). I think such calculations are
rather rare, especially for nucleic acids (with any software package).
Consider trying to dig up funds to obtain Amber12 and a GPU card. You might
compare that (probably about $1000 USD) to the value of the time you would
spend implementing a difficult method in an old version of Amber.
...good luck...dac
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Received on Fri Feb 01 2013 - 05:30:03 PST
