[AMBER] NAB to create DNA/RNA hybrid?

From: Jisha B <jisha.b.k0511.gmail.com>
Date: Sun, 26 Apr 2020 11:51:24 +0530

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 Sat Apr 25 2020 - 23:30:01 PDT
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