On Fri, May 11, 2012, natty yoshisawa wrote:
>
> I have generated DNA duplex (perfect matched) using NAB (AmberTools 1.5)
> with the following input:
>
> ----------------------------------------------
>
> molecule m;
>
> m = fd_helix( "abdna", "aagaaa", "dna" );
> putpdb( "nuc.pdb", m, "-wwpdb");
>
> -------------------------------------------------
>
> I got the duplex of sequence
> 5'-AAGAAA-3'
> 3'-TTCTTT-5'
>
> Next I would like to generate the single mismatch of the 3rd pair as
> 5'-AAGAAA-3'
>
> 3'-TTATTT-5'
>
> Could anyone please give me the input for NAB?
NAB doesn't have built-in commands to make mismatches. You could visit
w3dna.rutgers.edu, which has lots of useful DNA tools. Or, you could load
the WC duplex into xleap and use the erase and draw tools to modify the bases
by hand.
...good luck...dac
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Received on Sat May 12 2012 - 11:00:04 PDT
