AMBER: questions about RNA

From: <>
Date: Mon, 27 Jun 2005 22:19:58 -0500

Dear AMBER users:

   I am a new user of AMBER 8.0. Right now I am trying to do the MD simulation
with a piece of RNA molecule and also the hybrid of DNA:RNA duplex with the
complementary DNA sequence of the same RNA. The sequence of the single strand
RNA is 5' CCUGUAAUCUAGAAA 3', therefore the complementary DNA strand is
5' GGACATAGATCTTT 3'. Could I use nucgen to create the starting topology of
the ssRNA and the DNA:RNA hybrid, and how? I searched the Archive of this
topic but I could find any clear instruction about this problem. I have
learned the DNA-tutorial of AMBER 8.0 but I still have no idea about how to
play with RNA using nucgen. I will be very appreciate if you could answer this
question for me.

xinlei Huang

Chemistry department of Indiana University

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Received on Tue Jun 28 2005 - 04:53:01 PDT
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