AMBER Archive (2009)

Subject: Re: [AMBER] Custom RNA modeling

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Dec 08 2009 - 16:01:42 CST

Try MCSYM from Major's Lab. My friend modeled a 3D structure of a tRNA
like RNA. Good luck.

   Ilyas Yildirim, Ph.D.
   ---------------------------------------------------------------
   = Hutchison Hall B#10 - Department of Chemistry =
   = - University of Rochester =
   = 585-275-6766 (office) - =
   = http://www.pas.rochester.edu/~yildirim/ =
   ---------------------------------------------------------------

On Tue, 8 Dec 2009, Wallace Kunin wrote:

> I am looking to create models of RNA with sequencing that resembles tRNA.
> How do I create the pdb file I need or use leap to do this? I have tried
> using the sequence command but that does not allow for the RNA to take on
> the L shape that tRNA normally does but it just sequences bases in a wavy
> line pattern. I am guessing I need leap or nab to do this? Any help would
> be appreciated on how to do this or if I need to supply more information,
> let me know.
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