Re: AMBER: adding water molecules in lipid bilayer model

From: M. L. Dodson <>
Date: Mon, 09 Jul 2007 07:59:01 -0500

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 ( 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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 11 2007 - 06:07:24 PDT
Custom Search