AMBER Archive (2005)

Subject: AMBER: building nucleic acids

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Thu Jul 07 2005 - 23:07:03 CDT

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
molecules?

Thanks in advance
Mathew

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/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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