Re: AMBER: building nucleic acids

From: Bill Ross <>
Date: Fri, 8 Jul 2005 12:05:15 -0700 (PDT)

> 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.

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Received on Fri Jul 08 2005 - 20:53:01 PDT
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