AMBER Archive (2006)

Subject: Re: AMBER: water molecules with in 3 angstroms to the solute

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Jan 03 2006 - 03:05:24 CST

Dear Nagaraju,

If you just want to see the structure with water molecules that are 3A
within your structure, you can use VMD to do that. You need to play with
the representation part of VMD. Check out the VMD website for that.

Good luck,

On Mon, 2 Jan 2006, nag raj wrote:

> Dear Amber users,
> I solvated the solute with water
> (TIP3P) solvent, buffer radious is 10 angstroms. After
> MD simulations, i want to see water molecules within 3
> angstroms to the solute. Would you tell me how to do
> this.
> Thank you in advance.
> Happy new year.
>
> bye
> Nagaraju
>
>
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
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