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

Itamar Kass itamar.kass at monash.edu.au
Thu Jun 3 03:01:33 CEST 2010

Hi Tom,

Thanks for your replay. From the paper (DNA and lipid bilayers: 
self-assembly and insertion. J. Royal Soc. Int. 5, S241-S250, 2008. ) I 
understand that the DNA CG particles where identical to the one used for 
lipids and protein, am I correct? Also, they had used elastic network to 
hold them in place (instead of Secondary Structure used in proteins).


On 28/05/10 12:11 AM, Thomas Piggot wrote:
> Hi,
> 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.
> Cheers
> Tom
> 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


"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
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| Monash University,
| Victoria 3800
| Australia
| Tel: +61 3 9902 9376
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| E-mail: Itamar.Kass at monash.edu.au

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