[gmx-users] RNA MD Simulation using GROMACS

[Pruthvi Bejugam]

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