[gmx-users] CG (MARTINI) parameters for RNA

Thomas Piggot t.piggot at soton.ac.uk
Thu May 27 16:11:55 CEST 2010


The DNA parameters for use with the MARTINI forcefield are not publicly 
available to download at the moment, however they will be available very 
soon. I (or someone else from the Khalid group) will let the list know 
when and where they have been made available.



Itamar Kass wrote:
> Shalom all,
> I wish to try and simulate a protein with few RNA bases attached. As I
> favour speed over accuracy in this case I wish to use the MARTINI model.
> I could not find RNA/DNA parameters, but noticed that on the site there
> is a reference to Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP.
> DNA and lipid bilayers: self-assembly and insertion. J. Royal Soc. Int.
>   5, S241-S250, 2008.
> I wonder if someone had those parameters already implemented into the
> model? It will be nice to get it nicely packed. Or maybe even better,
> are there any beta parameters to RNA/DNA in a new MARTINI force field?
> All the best,
> Itamar

Dr Thomas Piggot
University of Southampton, UK.

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