AMBER Archive (2006)

Subject: Re: AMBER: help creating RNA

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Jun 22 2006 - 14:29:49 CDT

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_at_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
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - 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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