AMBER Archive (2006)

Subject: RE: AMBER: Umbrella sampling

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sun Jun 18 2006 - 11:57:09 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Ilyas Yildirim
> Sent: Saturday, June 10, 2006 11:54 PM
> To: amber_at_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
  ---------------------------------------------------------------
  - 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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