AMBER Archive (2009)

Subject: Re: [AMBER] Custom RNA modeling

From: case (case_at_biomaps.rutgers.edu)
Date: Mon Dec 14 2009 - 12:32:11 CST

On Mon, Dec 14, 2009, Wallace Kunin wrote:

> Just to rephrase and clarify this issue. I am looking to produce a few page
> simple instruction manual on RNA modeling and mechanics in AMBER.

It makes an enormous difference whether you want to explore the properties of
an RNA whose structure is already known, or whether you wish to create and
explore a model of an RNA with unknown structure.

Amber is primarily designed for the first task; MCSYM is primarily designed
for the second one. Neither task is especially amenable to making a "simple
instruction manual". My guess is that you need to be more explicit in
describing what you want to do (and why) in order to avoid inappropriate
responses from a mailing list.

...dac

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