Dear Atsutoshi,
I dont think that u can do this using AMBER. For nucleic acids, I am using
3DNA to reorient the structures.
On Sun, 18 Jun 2006, Atsutoshi Okabe wrote:
> Dear Ilyas,
>
> Thank you for your response.
>
> Particularly, I want to fix center of mass of one benzene molecule and
> center of mass another small molecule on z-axis. In addition, I want to
> restraint benzene plane vertically against z-axis through simulation.
> Can I do it with Amber ? If so, could you please tell me how to do ?
>
> Atsutoshi
>
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
> Ilyas Yildirim
> Sent: Saturday, June 10, 2006 11:54 PM
> To: amber.scripps.edu
> Subject: Re: AMBER: Umbrella sampling
>
> >
> > And I want to fix this two molecule on one axis (eg, fix their centers of
> > mass on y=0, z=0)
> >
> > How can I fix this two molecule on one axis with Amber program?
> >
> > I expect to give me any suggestions.
>
> Check out the program 3DNA, if your molecule is composed of nucleic acids.
>
>
--
Ilyas Yildirim
---------------------------------------------------------------
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- http://www.pas.rochester.edu/~yildirim/ -
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Received on Wed Jun 21 2006 - 06:07:06 PDT
