On Tue, May 17, 2011, Wu Xu wrote:
>
> I want to do MD simulation of 137 nt RNA by keeping phosphate groups
> neutral. I found from Amber Archive that RAN, RCN, RUN and RGN will keep
> the nucleotides of RNA neutral
The residues you mention are neutral because they lack phosphate groups, not
because the phosphate groups are neutral. If you want to (very artificially!)
have an RNA with a sugar phosphate backbone, but with no charges, you will
have to be prepared to define your own residues (or modify existing ones).
If you are new to Amber, I'd recommend learning on "real" systems,
probably starting with much smaller molecules. If you want to explore
non-physical systems (which can indeed be instructive) you still might
want to consider something smaller: 137 nt is rather large, and will take
a long time to simulate.
....dac
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Received on Tue May 17 2011 - 18:30:02 PDT
