[gmx-users] calculation radial concentration plots

[Felipe Merino]

Hi,

Check out RIcard Lavery's CANION, I think it'll do what you need.

There's the paper
http://nar.oxfordjournals.org/content/early/2014/06/06/nar.gku504.full

And the software
https://bisi.ibcp.fr/tools/curves_plus/canion-user-guide.html

Felipe

On 01/07/15 09:31, soumadwip ghosh wrote:
> Hi all,
>
>           I have been asked by one of my reviewers to calculate the number
> of excess cations surrounding a DNA duplex using radial concentration of
> the ions computed by integrating the grid-based concentration data within a
> cylindrical volume surrounding the DNA . I am actually trying to obtain
> curves like that of figure 7 in the link below-
>
> http://onlinelibrary.wiley.com/doi/10.1002/bip.22461/epdf
>
>
> Which are obtained from the radial concentration profiles. My question is
> how to make a radial concentration profile of say tetramethylammonium
> cations from some DNA groove/ backbone atoms and then obtain curves like
> that of figure 7 using equation 2 of the above reference.
>
> Thanks for your help in advance.
>
> Soumadwip Ghosh
> Research Fellow
> IITB
> India.

-- 
Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2306