> I want to do protein-RNA complex simulation. Can we simulate
> protein-RNA complex in AMBER. If so, what is the force field that we should
> use. How far it is different from doing Protein simulation and Nucleic acid
> simulation??
Yes, you can simulate a protein-RNA complex. Which force field is a
matter of debate and often a valid research question. Normally I would
suggest using the latest force fields, such as ff14SB and the
ff99+bsc0+chiOL3, or basically the defaults that current versions of AMBER
recommend since this is usually the consensus best guess at the time of
release.
How is it different from doing protein simulation and nucleic acid
simulation? Perhaps it is not clear, but to me it is equivalent to doing
a combined protein and nucleic acid simulation. The difference is that
you have proteins *and* RNA in the simulation. Probably salt and water as
well. One might also argue that sampling could be more difficult and
there is a greater chance of failure depending on initial conditions since
you could have problems with either the initial protein or RNA model, or
where the salt is, ... However, to answer these questions and understand
the differences, you have to try the simulations out. There is no way up
front to provide advice since we have no idea what simulations you want to
run, what you are trying to learn, or what your experience is. Simple
answer: Yes, AMBER can do protein-RNA complexes. Long answer: It is wise
to understand what you are trying to learn, how you will assess and
validate the simulation results, and, first, do you at least know the
basics of the methods?
If you still have questions, I strongly recommend trying out the AMBER
tutorials and learning how to setup simulations, how to run simulations,
and importantly, how to analyze the simulation results.
--tec3
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 04 2016 - 20:30:04 PST
