Re: mutation of DNA

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Thu Jul 15 2010 - 10:56:27 CDT

3dna from wilma olson at Rutgers or curves from richard lavery at IBCP
are nice tools for manipulating and analyzing DNA structures.

to "mutate" DNa you can
do following
extract DNA helical parameters of a given PDB snapshot using 3DNA
The output is a ".par" file.
Then change the basepair in question in the ".par" file and use it to rebuild
a PDB file.

such a XYZ -> PAR -> XYZ conversion introduces an RMSD error less than 1A
between the initial XYZ and final XYZ structures (if you don't mutate the
sequence)

If you are looking for some sort of chemical perturbation scheme that's
another story.

Tom

On Thursday 15 July 2010 05:57:46 am sudipta wrote:
> Hi All,
> Is it possible to mutate DNA base pair by psfgen or VMD? Any suggestion
> will be highly appreciated.
>
> Thanks and regards
> Sudipta
>

*******************************
   Thomas C. Bishop
    Tel: 504-862-3370
    Fax: 504-862-8392
http://dna.ccs.tulane.edu
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