[gmx-users] How to make a TM protein - Help

[Jose D Faraldo-Gomez]

Hi,

Have a look at Europ. Biophys. J 2002 31: 217-227 for a methodolgy for 
setting up membrane protein-lipid interfaces in MD simulations. Let me know 
if this interests you and I'll send you the source code.

Jose

NB: compatible with gromacs 2.0 only


>From: "J Simms" <JXS818 at bham.ac.uk>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] How to make a TM protein - Help
>Date: Mon, 22 Jul 2002 15:45:48 +0100
>
>Hi all,
>	I am working on a G protein coupled receptor, and would like to
>run a series of MD runs on the helicies. I have followed the tutorial
>and can do these runs in SPC water, but I would now like to do
>similiar runs in a membrane domain. As I understand it I can obtain
>lipid topologies from the net, my question is how do I a) use these
>topoligies and b) make a hole/channel in the lipid for my protein to
>sit. Once that is done how do I then place the protein in the
>channel in the lipid. I am VERY new at this any any help would be
>greatly appreciated!
>
>Many Thanks in Advance
>
>John Simms
>
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