AMBER Archive (2009)

Subject: Re: [AMBER] Circular RNA topology file

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Oct 21 2009 - 14:06:17 CDT

On Wed, Oct 21, 2009, Kasprzak, Wojciech (NIH/NCI) [C] wrote:
>
> I am trying to prepare a circular RNA molecule (such as, for example
> PDB# 2OIU) for an MD run. I was able to produce the prmtop and
> inpcrd files in xleap by editing out the H5T, H3T and the RX5 and
> RX3 designations that xleap placed there in the first pass (without
> removing the first (in the pdb file) nuleotide's phosphate group). RNA
> minimization worked fine, but during the equilibration in solvent the
> last-to-first nucleotide backbone connection (O3' - P) "drifted apart,"
> suggesting that the topology file most likely is not correct.
>
> Does anyone know the correct procedure I should follow, and, if so,
> could show

First, modify the leaprc file to remove the addPdbResMap commands that give
you 5' and 3' terminal nucleotides in the first place (since they don't exist
in circular RNA). So change a line like:

  { 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" }

to

  { "G" "RG" } { "GN" "RGN" }

Second, be sure to use the "bond" command to add the O-P bond that completes
the circle. Visualize the result in xleap to be sure that exactly the bonds
that you want are there. Or, you can load the prmtop file into VMD and that
can also be used to visualize the bonding.

...dac

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