Thank you very much for your reply. Unfortunately, my polymer is made of
protein monomers, not nucleic acids, and it looks like 3DNA works only for
nucleic acid structures. Does anyone have any suggestions on how to reorient
the molecule within AMBER? Since XLeap already reorients the molecule when
it creates the solvent box, it seems like it might be possible to change the
XLeap source code in order to make it orient the polymer along the z-axis.
However, I am not familiar with the XLeap source code and I would have no
idea where to begin. If anyone has any suggestions I would be very grateful.
Thanks,
Kenley
On 3/8/06, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:
>
> 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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Received on Sun Mar 12 2006 - 06:10:16 PST
