Re: [AMBER] dna with different base pairs/turn

From: Jio M <jiomm.yahoo.com>
Date: Mon, 11 Nov 2013 10:01:33 -0800 (PST)

Dear David and Rodrigo

Thanks for reply... I used nab and hopefully doing correct (almost taken from manual) as shown below


molecule m; string seq; string cseq;
seq = "aaaaaaaaaaaaaaaaaaaaaaaaaa";
cseq = wc_complement( seq, "", "dna" );
m = wc_helix( seq, "", "dna", cseq, "", "dna", 2.25, -4.96, 34.28.0, 3.38, "s5a5s3a3" );
putpdb ("test.pdb",m);


I have further two queries:


1) Is it really necessary to use bdna ( ) function here. I could not compile with bdna () using programme like this (always getting some syntax error, though I expect same result):

string seq;
seq = "aaaaaaaaaaaaaaaaaaaaaaaaaa";
bdna (seq)
{molecule m;string cseq;
cseq = wc_complement( seq, "", "dna" );
m = wc_helix( seq, "", "dna",cseq, "", "dna",2.25, -4.96, 34.28, 3.38, "s5a5s3a3" );
putpdb ("test.pdb",m);
};


2) For 10.5 bp/turn I changed the twist from 36 to 34.28. I dont know what would be the ideal params for 10.5 bp/turn B-DNA. Should I keep the xoffset (2.25 ), inclination (-4.96 ) 3.38 rise same?


Thanks

Jiomm





On Monday, November 11, 2013 2:23 PM, David A Case <case.biomaps.rutgers.edu> wrote:
 
On Sun, Nov 10, 2013, Jio M wrote:
>
> I want to generate a BDNA with 10.5 bp/turn against 10bp/turn (bdna
> in NAB). I checked online few websites to build such DNA but it needs
> other parameters as well to customize own DNA (rise,tilt,twist, and many
> more).
> Anyone has better idea to generate 10.5 bp/turn DNA?

In addition to the response already posted, you could look at Section 15.12
of the AmberTools Manual "Creating Watson-Crick Duplexes". The wc_helix()
routine allows the user to input the desired twist.

...dac



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Received on Mon Nov 11 2013 - 10:30:02 PST
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