AMBER Archive (2004)

Subject: Re: AMBER: nucgen generated RNA duplex: leap problems

From: Arvind (arvind_at_mbu.iisc.ernet.in)
Date: Wed Apr 21 2004 - 15:23:28 CDT

Thanx Dave & Bill, that G-11 was an error of mine, should have been C. I
can see that there are 2 G-G pairs (because of G-11) but there is no U-U
pair.

Secondly i did not use nukit to generate the input file.

Regards,
Arvind.

On Wed, 21 Apr 2004, Bill Ross wrote:

> Minor correction or amplification to Dave's point - there are
> actually 2 G-G base pairs here, since strands go 5' -> 3' --
> and also a U-U in the middle:
>
> C5 G C A A A U U U G G G3
> ^^^ ^^^ ^^^
> 1 2
>
> C5 G C A A A U U U G G G3
> ^^^ ^^^ ^^^
> 2 1
>
> On another note, was nukit used to generate the input file?
> Although there is a suggestion to drop it from future releases,
> I have modified it to no longer write the link.in file since
> prep/link/edit/parm have been replaced by leap, and perhaps
> it should be just incorporated into nucgen itself.
>
> Bill
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