[AMBER] RNA Simulation

From: jacob wick <jacobwick.la.gmail.com>
Date: Thu, 12 Mar 2015 23:58:59 +0530

Hi all,
I am trying to simulate a chunk of RNA molecule (20 residues) to predict
its tertiary structure. The crystal structure of that RNA is not available,
so I don' t know how that chunk will finally look like.

I am creating that 20 residues chuck by NAB and then I am simulating it for
100 ns as per the AMBER TUTORIAL B1 with all_nuc94_ol_bsc0.in (ht tp://
fch.upol.cz/en/rna_chi_ol/) force filed. Within few ns, I am getting a
pseudoknot structure, after which tere is no significant change in rmsd.
The rmsd difference between the initial structure (created by NAB) and the
md average structure is around 52 (after re-imaging by cpptraj) which is
constant from 5ns to rest of the simulation period.

Please suggest what can I do to make my RNA simulation more reliable. Is
the protocol used by me is right?

Can I justify the huge change in the rmsd as I am starting with a streach
created by NAB and finally I am getting a stable tertiary structure. So, as
these two structures are quite different from each other, leads to a large
change in the rmsd value?

Thanks and Regards,
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Received on Thu Mar 12 2015 - 11:30:05 PDT
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