AMBER: building nucleic acids

From: mathew k varghese <>
Date: Fri, 8 Jul 2005 05:07:03 +0100 (BST)

Dear AMBER users,

I have some questions about building starting
structures for simulations.

How can I build nucleic acids with bulges, mismatches
etc.? Could I use NUCGEN for this?
How can I change the conformation of a particular base
say, a bulge in a crystal structure (looped out
conformation to stacked in) without altering the
otherbases? Is there any software available for this.
How can I build complexes of nucleic acids with small

Thanks in advance



Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
Kottayam, Kerala



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Received on Fri Jul 08 2005 - 05:53:00 PDT
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