Re: [AMBER] NAB to create DNA/RNA hybrid?

From: Satyaseelan C <>
Date: Tue, 28 Apr 2020 09:08:27 +0530

Dear Jisha,

   I would like to suggest 3D-NuS (,, for building DNA-RNA hybrid
structures. The structural parameters used for modeling hybrid structures
are derived from DNA-RNA hybrid structures deposited in the PDB.

On Sun, 26 Apr, 2020, 11:54 AM Jisha B, <> wrote:

> Respected all,
> Since I am a beginner in AMBER, I wonder if we could use the following
> procedure to create DNA/RNA hybrid duplex?
> Use the following script(as in the tutorial) to create a duplex and then
> edit the dT in the complementary strand to rU in the text file and load it
> to xleap and visualize. Would that work? Would such a a system be
> considered as a DNA/RNA hybrid? I have the doubt because literature
> suggests that the hybrid may not be strictly A type or B type. Also what
> would be the force field considerations in such a hybrid?So how to proceed
> in this. Thank you for any help you can provide.
> molecule m;
> m = fd_helix( "abdna", "aaaaaaaaaa", "dna" );
> putpdb( "nuc.pdb", m, "-wwpdb");
> --
> Jisha B.
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Received on Mon Apr 27 2020 - 21:00:03 PDT
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