AMBER Archive (2005)

Subject: Re: AMBER: building nucleic acids

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Sat Jul 09 2005 - 00:55:00 CDT

Dear AMBER users,

For building non-standard nucleic acids and for
manipulating experimental structures structures can I
use NAB? Is it very difficult to try it? Or could you
suggest some other software.
Mathew
--- Bill Ross <ross_at_cgl.ucsf.edu> wrote:

> > How can I build nucleic acids with bulges,
> mismatches
> > etc.? Could I use NUCGEN for this?
>
> NUCGEN only builds helices, though you can include
> mismatches.
>
> You can use a graphical manipulation program such as
> leap or
> something more powerful. In any case iteratively
> moving atoms
> or rotating bonds then holding parts of the
> structure fixed
> while energy minimizing others to clean up.
>
> Or perhaps there is software to build what you want
> from some
> sort of specification.
>
> Bill
>
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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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