[gmx-users] Which POPC Bilayer to start?

[Jim Fonseca]

I've had success with Tieleman's lipids.  I used popc128b.pdb. Since  
it has the extra ns of equilibration, I figured it would cause fewer  
problems.  However, once you start messing around with making hole in  
the membrane and adding a protein, you'll need to re-equilibrate  
again (EM & PR).

Jim

On Sep 20, 2006, at 5:48 PM, Akshay Patny wrote:

> Hi All
>
> I am trying to use POPC bilayer for doing GPCR simulation.
>
> I have come across two options of generating a POPC bilayer >>>>
>
> 1. I can generate a POPC bilayer from the VMD Membrane plug-in,  
> wherein the
> membrane is generated from the pre-built membrane square patches  
> and lipid
> tails are (almost) fully extended.
> 2. Alternatively, I can download the pre-equilibrated POPC bilayer  
> from Dr.
> Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People
>
> Since, I am new to the GPCR-membrane modeling, can you suggest me  
> which out
> of the above two options can be a better starting point for the  
> simulation
> of my GPCR protein? A membrane generated from VMD or a pre- 
> equilibrated
> membrane?? Would the equilibration time for my protein be lesser in  
> one out
> of the two?
>
> If option 2 is a good idea then out of popc128a.pdb and  
> popc128b.pdb (both
> available from Prof. Tieleman's website), which will be a better  
> model to
> start with?
>
> Thank you very much in advance.
> Akshay
>
> Akshay Patny
>
> Graduate Research Assistant
> Faser Hall 417, Department of Medicinal Chemistry
> Research Institute of Pharmaceutical Sciences
> University of Mississippi
> University, MS 38677
> E-mail: akshay17 at olemiss.edu
> Tel: 662-915-1286 (office); Web: www.olemiss.edu
>
>
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