[gmx-users] membranes & proteins revisited

Alan Dodd anoddlad at yahoo.com
Wed Dec 19 13:58:16 CET 2007

Of course it's unnatural, it's a membrane made of gas instead of lipid ;)  I'd recommend that you equilibrate the "membrane" first, and check it actually behaves in a manner close enough to one for what you want - and then insert a protein into it.  You might want to look into the make_hole suite on the user contributions page, it's designed to make a hole in a lipid membrane for a protein, but I'm sure modifying it for argon would be rather trivial.

----- Original Message ----
From: Magnus Andersson <magnus.andersson at chalmers.se>
To: gmx-users at gromacs.org
Sent: Tuesday, December 18, 2007 9:38:09 PM
Subject: [gmx-users] membranes & proteins revisited

Hi all,

I have a trimer membrane protein structure & an artificial Argon grid
membrane (100x100x30Å).

First I wonder whether you should equilibrate the membrane first (it looks
very un-natural, like a perfect grid...) and then physically remove atoms
where I want to have my protein, then run:
genbox -cp protein.gro -cs membrane.gro

if I just run it as it is, I get:

Checking Protein-Solvent overlap: tested 1512 pairs, removed 9261 atoms.

I feel I'm getting there, but need some advice to come to the point where
I have my trimer in a "relaxed" membrane...

Thanks /

Magnus Andersson

Chalmers University of Technology
Dept of Chemistry and Biological Engineering
Email: magnus.andersson at chalmers.se
Homepage:  http://www.csb.gu.se/neutze/
Phone: +46 (0)31-786 3917
Fax: +46 (0)31-786 3910
Lundberg Laboratory
Medicinaregatan 9e
SE-413 90 Göteborg

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