AMBER Archive (2006)

Subject: Re: AMBER: aligning polymer with Z-axis of periodic box

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Mar 08 2006 - 16:54:22 CST

Dear Kenley,

I am using the program 3DNA to reorient my structure when I need it. Here
is the website of this program:

http://rutchem.rutgers.edu/~xiangjun/3DNA/

Using this program, u can reorient any structure which has the known
residues in it. Hope this helps. Good luck...

On Wed, 8 Mar 2006, Kenley Barrett wrote:

> Dear AMBER community,
>
> I am simulating a helical polymer using explicit solvent and periodic
> boundary conditions. Due to some stuff that I want to do with the periodic
> boundary conditions, it is crucial that the long axis of the helix be
> parallel to the z-axis of the periodic box. I know that XLeap reorients the
> molecule in cartesian coordinate space when it creates the solvent box, but
> I don't know how this reorientation works or how to modify it afterwards so
> that the long axis of the helix ends up parallel to the z-axis. Does anyone
> have any suggestions?
>
> Thank you all in advance for your help.
>
> Sincerely,
> Kenley Barrett
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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