VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jan 02 2018 - 10:48:52 CST

The dumb way (which is where I would start), is just to rename the ADE residue into URA (or whatever it says in the topology file), and rebuild the psf. Atoms that don't have the same name in both residues will be ignored. However, the hydrogen bonding you want is impossible. T converts cleanly to U, not A to U. A->U is replacing a 2-ring base (purine) with a 1-ring base (pyrimidine), so they won't fit nicely and hydrogen bond like you want them to.
-Josh

On 12/30/2017 12:18 PM, parinaz bashirbanaem wrote:

 Hi everyone,

I'm working with DNA-RNA complex and trying to convert an adenine group into an uracil in RNA strand. In addition to, I want to retain hydrogen bonding (Watson-crick) between aforementioned uracil and thymine (in DNA strand) after conversion. Could anyone lead me towards how to perform this task?

Thank you very much for any suggestion.

Best regards,