AMBER Archive (2007)

Subject: Re: AMBER: adding water molecules in lipid bilayer model

From: M. L. Dodson (mldodson_at_houston.rr.com)
Date: Mon Jul 09 2007 - 07:59:01 CDT

Vijay Manickam Achari wrote:
> Dear amber users,
>
> I have built bilayer system. Now I want to solvate the
> bilayers with water. I want to put a layer of water
> molecules, say 250 water molecules on top and bottom
> of the bilayer.
>
> How am I suppose to put the water molecules?
> Is there any command available in Amber so that I can
> put only on top and bottom of my bilayer.
>
> If I use solvatebox, it puts all around my bilayer
> system which I dont want like that.
>
> Can anyone help me??
>
> Thank you
> Vijay Achari
>

Packmol (http://www.ime.unicamp.br/~martinez/packmol/) was written
to generate starting configurations for molecular dynamics. IIRC
one of the examples on the web site does what you want (differing
only in the details).

Bud Dodson 

-- 
M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-five_63-386_one
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