On Wed, Jul 27, 2011 at 3:33 PM, Anjan Dwaraknath <anjandn.gmail.com> wrote:
> Hello
>
> I have problem regarding NAB
> I want to use wc_helix function in NAB to create A-RNA double helix,
> I have two issues :
>
> 1) I want to know what are the right parameters to use in wc_helix to get
> A-RNA structure
>
> 2) When I use the wc_helix function for RNA,
> I am not getting the right basepairs in the output PDB file.
> It seems to use a ADE-ADE base pair instead of ADE-URA
> Here is the code I used
>
> //To create A-RNA double helix
> molecule m;
> string seq,cseq;
>
> seq= "aaa";
> cseq="uuu";
> m = wc_helix( seq, "", "rna" , cseq , "", "rna",6.0, 20.0, 33.0, 2.8,
> "s5s3" );
>
> putpdb( "test.pdb", m );
> //end
>
> I checked the source code of wc_helix given in the AMBER manual ,
> It seemed to ignore 'u' characters as it had only these definitions
> (line no. 38)
> loup["g"] = "G"; loup["a"] = "A";
> loup["t"] = "T"; loup["c"] = "C";
>
> But then I checked the wc_helix.nab it had
> (line no. 26)
> loup["g"] = "G"; loup["a"] = "A";
> loup["t"] = "T"; loup["c"] = "C"; loup["u"] = "U";
>
> I guess that is not the problem.
> So I am confused about what the problem is.
>
> Can you please help me.
>
> Thank you for your time.
>
> Anjan Dwaraknath
> Third Year Btech, Engineering Phyiscs
> Indian Institute of Technology Madras
>
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Received on Wed Jul 27 2011 - 04:00:03 PDT
