AMBER Archive (2004)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Apr 21 2004 - 13:33:00 CDT

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prep/link/edit/parm have been replaced by leap, and perhaps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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