[gmx-users] RNA MD Simulation using GROMACS

Erik Marklund erikm at xray.bmc.uu.se
Mon May 20 11:56:07 CEST 2013


To get useful help with this issue you need to provide a more informative description of what when wrong, i.e. what gromacs tool was invoked and what input was used.


On 20 May 2013, at 10:59, Pruthvi Bejugam <pruthvi.nccs at gmail.com> wrote:

> Hi all,
>                I want to perform a RNA (Just RNA no protein or DNA
> included) MD Simulation. Can anybody suggest me what are the general
> parameters should be used for the RNA MD Simulations.
> I know that AMBER and CHARMM force field work well for DNA and RNA. i have
> tried the RNA MD simulation using AMBER force field and it got failed and
> the error was "FATAL error found no suitable atoms in the parameters." so,
> any one please help me out with this problem.
> Thanks In advance,
> --
> Pruthvi Raj. B,
> JRF, Lab no. 9 (New Building),
> Computational and Systems Biology Lab,
> National Centre for Cell Science,
> UoP Campus, Ganeshkhind,
> Pune, Maharashtra, 411007
> -- 
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