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

[Itamar Kass]

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).

Best,
Itamar

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

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| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
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