On Thu, Jul 20, 2017, Mary Varughese wrote:
>
> I want to understand how the ion distribution around DNA changes upon
> a ligand binding in simulation of DNA-ligand complex. Could any one
> suggest a method to do this.
A couple of methods are described in this paper:
%A G.M. Giambasu
%A T. Luchko
%A D. Herschlag
%A D.M. York
%A D.A. Case
%T Ion counting from explicit solvent simulations and 3D-RISM
%J Biophys. J.
%V 104
%P 883-894
%D 2014
But, basically, for MD you analyze ions in the same way you analzye water.
> Also when i do grid analysis of water i have created a Na.explorer
> also. But i dont know how the range should be given (in water analysis
> we would say 2 or 3 times bulk water density). Is grid analysis of Na+
> ions a suitable approach? if i add both Na+ and Cl- ions, should i
> create .explorer for both Na+ and Cl- ?
The range (relative to bulk density) is likely to be higher for ions than
for waters. You should just use cpptraj to create a grid (for both anions
and cations, although the anion distribution around DNA has relatively
few features), and use some visualization program to see what the ranges
are. (VMD and Chimera are fine, but other visualization programs will
work as well.) Be aware that you need lots more sampling to converge ion
distributions than to converge water distributions (since water is at 55 M
but your salt is probably only something like 0.1 M.)
...good luck...dac
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Received on Thu Jul 20 2017 - 05:00:02 PDT
