Re: [AMBER] newbie question: simulating miRNA

From: David A Case <>
Date: Fri, 31 Aug 2012 15:44:25 -0400

On Fri, Aug 31, 2012, Niel Henriksen wrote:
> The standard nucleic acid residues in AMBER were not
> parameterized to include a 5'-phosphate. You would need
> to create a new residue for this (mol2 and frcmod files for
> charges and parameter info respectively).

You can get a 5' phosphate group by using OHE as the 5' residue, e.g.:

  x = sequence { OHE C A G U }

will create an RNA strand with a 5' (protonated) phosphate group. However,
I'm not sure how much this has been tested for accuracy (it basically uses the
same parameters for the terminal phosphate as for the bridging phosphodiesters
in the rest of the strand.) Also, the fd_helix() routine in NAB doesn't know
about this capping group, so you may need to jump through some hoops (as
described in the original post) to get a starting structure.


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Received on Fri Aug 31 2012 - 13:00:03 PDT
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