There is no PDB file available in the protein data bank, so I have to create the PDB file. Can anyone help me please?
Michal H. Kolář
I point you to the Nucleic Acid Builder of Ambertools (http://ambermd.org/doc12/AmberTools13.pdf), in the manual especially to Sec. 18. However, it might be a bit tedious...
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Ilyas Yildirim
Another way of creating such a .pdb file is by doing homology modeling. There are NMR and xray structures of Hoogsteen base pairs, and you can simply use those xyz coordinates of the heavy atoms to replace the Watson-Crick base pairs.
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