Dear Prof. David Case and Bud Dodson,
Thank you very much for replying. I posted this question because in the AmberTools 1.5 manual (pdf file page 241, section 13.5.1) stated that NAB can create mismatched base pairs.
By the way, I will prepare a mismatched duplex as your suggestion.
Regards,
N. Yoshisawa
> From: mldodson.comcast.net
> Date: Sat, 12 May 2012 14:40:13 -0500
> To: amber.ambermd.org
> Subject: Re: [AMBER] How to generate single mismatch DNA duplex using NAB
>
>
> On May 12, 2012, at 12:48 PM, case wrote:
>
> > 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
> >
> >
>
>
> I have done this by using nab to create a matched DNA which is what is desired
> except for the mismatch. Then put the PDB into a text editor, delete the base
> substituent decorations (or the whole base if it is a pyr<->pur mismatch),
> and change the name of the residue to what is desired. Leap will rebuild the
> base when you read in the PDB. Careful initial minimization/equilibration will
> be needed.
>
> Bud Dodson
> --
> M. L. Dodson
> Business email: activesitedynamics-at-gmail-dot-com
> Personal email: mldodson-at-comcast-dot-net
> Gmail: mlesterdodson-at-gmail-dot-com
> Phone: eight_three_two-five_63-386_one
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 13 2012 - 21:00:03 PDT
