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/ -
---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Mar 12 2006 - 06:10:16 PST
