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

Itamar Kass Itamar.Kass at monash.edu
Thu May 27 07:54:00 CEST 2010

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,


"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu.au

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