Akshay Patny wrote:
Dear All
I am trying to simulate a class A GPCR model in presence of a lipid
bilayer. For that, I am trying to prepare my initial system consisting
of Protein + Pre-hydrated Lipid bilayer + Counter-ions.
Since I would be using GROMACS 3.3.1, I am planning to use the
pre-hydrated lipid bilayer available through Prof. Peter Tieleman’s
website:
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
I am curious what kind of bilayer should I use out of DPPC, DMPC, POPC
available? Does some lipid bilayer provide certain advantages over
others for simulation of GPCRs?
I appreciate any suggestions regarding the same.
DPPC, DMPC and POPC are different bilayers but in what
conserns GPCR simulations you can use DPPC and POPC
without problem. DMPC would be a bit too short !!
Note that you should consider looking up in the literature and
see wehter there is any info conserning the type of lipid
embedding your GPCR !!
XAvier
--
----------------------------------
Xavier Periole - Ph.D.
Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel: +31-503634329
Fax: +31-503634398
email: [EMAIL PROTECTED]
web-page: http://md.chem.rug.nl/~periole
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