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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Received on Sat May 12 2012 - 13:00:03 PDT
