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 Madras
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Received on Wed Jul 27 2011 - 03:30:03 PDT
