Dear Seth,
u can use nucgen to create an RNA structure. Here is an example of a
nucgen input file:
---------------- nucgen.in ---------------------
5'GACC3' A-Form RNA: STRAND 1
R
G5 A C C3
5'GACC3' A-Form RNA: STRAND 2
R
G5 A C C3
END
$ARNA
------------------------------------------------
This will create a (GACC)_2 ARNA structure (Look pp.236 of AMBER8 Manual
for more info). U can modify this nucgen.in file to create your own
structure. Hope this helps.
Best,
On Thu, 22 Jun 2006 sethl.gatech.edu wrote:
>
>
> --
>
> Dear all,
>
> I have been fighting with leap in trying to build a simple RNA molecule. I've
> been creating a DNA molecule and then modifying the .pdb file by changing the
> residue names from "A" to "RA" for instance, but leap seems to complain quit a
> bit. Can some one give me a quick protocol as to how to create an RNA molecule?
>
> Thanks,
> Seth Lilavivat
> Georgia Institute of Technology
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--
Ilyas Yildirim
---------------------------------------------------------------
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- University of Rochester - -
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- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Jun 25 2006 - 06:07:14 PDT
