AMBER Archive (2006)

Subject: Re: AMBER: A dummy atom on the center of solute molecule

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon May 22 2006 - 06:58:24 CDT

Can you explain a little bit more on the structure and the dummy atom? Is
it going to be part of the solute, or is it going to have some distance
restraints to keep it in a particular region of the solute?

On Mon, 22 May 2006, Atsutoshi Okabe wrote:

> Dear all.
>
>
>
> Hi.
>
> I want to do umbrella sampling MD along the reaction coordinate between
> protein and
>
> the center of ligand molecule.
>
> So I need to set a dummy atom on the center of ligand molecule.
>
> How should I put a dummy atom in pdb file in Amber8?
>
>
>
> Could you please give me any suggestions?
>
> Thank you.
>
>
>
> Acci Okabe
>
>
>
> 

-- 
  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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