I want a PDB file of DNA sequence I am interested in (10 base pairs) for docking. I will appreciate if any of you can please clarify some of my doubts.

Do you think, I can generate PDB file by using this link http://www.scfbio-iitd.res.in/software/drugdesign/bdna.jsp

I did generate the PDB file using the above site. However, when I am using that PDB file for docking it do not give accurate results. It just fits to the sequence and it lacks the information the PDB file downloaded from protein data bank has.

How can I get the pdb file of the DNA sequence I want from protein data bank, I did search it but did not find the one I want. Is it a way to extract the PDB file?

What are other methods I can use to generate PDB file of B-DNA sequence?

Thank you for your time.



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