Re: area per lipid for a protein embedded membrane system

From: Nicolas Sapay (n.sapay_at_ibcp.fr)
Date: Sat Mar 11 2006 - 04:42:32 CST

Hi,
Well in this case I may have something that can help you. It is a python
script that I have written some months ago. Unfortunaly, It works with
the MDtools python library (no longer developped), is awfully coded and
incredibly slow :-). Basically, the script projects each lipid on a grid
and count the bins filled by the projection. This tends probably to
over-estimate the area per lipid; a Voronoï tessellation would probably
be a better method.

Nico

enjoy

Le ven 10/03/2006 à 19:25, M. Madhu a écrit :
    Hi Nicolas,
    
    What I meant is "transmembrane protein in a membrane sytem". Thank you.
    
    Madhu
    
>From: nsapay_at_ibcp.fr
>To: "M. Madhu" <madhu7_at_hotmail.com>
>CC: namd-l_at_ks.uiuc.edu
>Subject: Re: namd-l: area per lipid for a protein embedded membrane system
>Date: Fri, 10 Mar 2006 19:08:54 +0100
>
>Hello Madhu,
>What do you mean by embedded? You mean the protein is transmembrane or just
>inserted in the membrane interface as the Prostaglandin H2 synthase?
>
>Nicolas
>
>Selon "M. Madhu" <madhu7_at_hotmail.com>:
>
> >
> > Hi All,
> >
> > Could someone share a script file for calculating area per lipid
> > for a membrane protein embedded in a bilayer system? Or, any
> > suggestions to measure it? Thank you.
> >
> > Madhu
> >
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-- 
[ Dr Nicolas Sapay ]
Institut de Biologie et Chimie des Proteines
CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
Phone: +33 (0)4 72 72 26 46 - Fax: +33 (0)4 72 72 26 04
Address: 7 passage du Vercors,  69367-F Lyon cedex 07, France

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