Re: [AMBER] How to generate single mismatch DNA duplex using NAB

From: Charles Johnson <cjohns98.slu.edu> Date: Mon, 14 May 2012 07:41:19 -0500

----
Charles A. Johnson
Ph.D. Candidate
Department of Chemistry
Saint Louis University
Monsanto Hall 214
3501 Laclede Ave.
St. Louis, MO  63103-2010
Fax: (314) 977-2521
Email: cjohns98.slu.edu
On May 13, 2012, at 10:30 PM, natty yoshisawa wrote:
> 
> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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