Heard that RNA/DNA system could be a little trickier than proteins due
to the many negative charges.
I found somewhen a nice article about RNA simulations in general.
Probably some questions you have / will have are answered there:
A short guide for molecular dynamics simulations of RNA systems
Yaser Hashem, Pascal Auffinger
Methods 47 (2009) 187–197
greetings
thomas
Am 04.07.2012 16:52, schrieb gmx-users-requ...@gromacs.org:
On 7/4/12 6:45 AM, Ravi Raja Merugu wrote:
> Hello every one,
>
> Im interesting in performing a MD for Protein - RNA complex , Can any
> one suggest a good tutorial.
>
Such systems do not differ significantly from simulations of simple proteins in
water, since pdb2gmx can produce topologies for both proteins and nucleic acids.
The remaining workflow is basically the same.
-Justin
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