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

From: David A Case <case.biomaps.rutgers.edu>
Date: Mon, 11 Nov 2013 15:22:55 -0500

On Mon, Nov 11, 2013, Jio M wrote:
>
>
> 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);
>
>
>
> 1) Is it really necessary to use bdna ( ) function here.

No.

> 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?

I have no idea what the other parameters should be. The answer must depend
on what information you have and what you are going to use the structure for.

...dac


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Received on Mon Nov 11 2013 - 12:30:03 PST
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