AMBER Archive (2006)

Subject: AMBER: Which POPC Bilayer to start?

From: Akshay Patny (
Date: Wed Sep 20 2006 - 16:48:42 CDT

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,

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 Patny

Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
Tel: 662-915-1286 (office); Web:

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