Re: [AMBER] area per lipid popc membrane

From: Dickson, Callum <callum.dickson09.imperial.ac.uk>
Date: Thu, 23 Aug 2012 09:12:14 +0000

Hi,

Some time ago I used the HOLE program to calculate the pore radius of a transmembrane channel:

http://www.msg.ucsf.edu/local/programs/hole/doc/hole_d00.html

I'm not sure whether this will be suitable for your system or not (since it is intended for channels through proteins, rather than channels through membranes) but possibly worth a look.

Cheers,

Callum
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Albert [mailmd2011.gmail.com]
Sent: 23 August 2012 06:52
To: AMBER Mailing List
Subject: Re: [AMBER] area per lipid popc membrane

On 08/23/2012 07:19 AM, jojartb.jgypk.u-szeged.hu wrote:
> Hi,
> Another possibility is to use the GridMAT-MD tool:
> http://www.bevanlab.biochem.vt.edu/GridMAT-MD/
> The program needs only a xxx.gro file, which can be produce by using vmd.
> HTH,
> Balazs

the results from GridMAT-MD is not reliable for protein/membrane system
since it overestimate protein area. I tested it for protein/POPC system,
you always get something around 54 for ALP which is also state in J
Comput Chem 31: 21692174, 2010 titled "g_membed: Efficient Insertion of
a Membrane Protein into an Equilibrated Lipid Bilayer with Minimal
Perturbation". here is a figure for ALP in g_membed paper:

https://dl.dropbox.com/u/56271062/figure3.jpeg

for protein free system, it should be all right.

good luck

Albert

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Received on Thu Aug 23 2012 - 02:30:03 PDT
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