AMBER Archive (2009)
Subject: Re: [AMBER] lipid bliayers
From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Wed Mar 18 2009 - 08:17:04 CDT
On Wed, 2009-03-18 at 14:00 +0100, Urszula Uciechowska wrote:
> I was wondering, if maybe someone of you know how to make a hole in lipid bilayer and place the
> protein? Have someone maybe a script for that?
One publications that comes to mind is
http://www.ncbi.nlm.nih.gov/pubmed/17367719?dopt=AbstractPlus . (The
programs they developed are however based on GROMACS)
In many cases you may be able to just use your favorite visualisation
program and remove unwanted lipids.
An additional option may be to start with a coarse-grained model to
speed up the equilibration process. But I am not aware if anybody used
one of the various models out there with AMBER and if it would be
straightforward to use them with AMBER (exclusions?).
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