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<p><font face="Tahoma">Hi Saumya,</font></p>
<p><font face="Tahoma">for topology please look at those two paper from</font><font
face="Tahoma"> Poger in which he derive new parameters for various
lipids:</font></p>
<p><font face="Tahoma">1. Poger D., van Gunsteren W. F. & Mark A.
E. (2009) A
new force field for simulating phosphatidylcholine bilayers. J. Comput.
Chem. in press (doi: 10.1002/jcc.21396)</font></p>
<p><font face="Tahoma">2. Poger D. & Mark A. E. (2010) On the
validation of molecular
dynamics simulations of saturated and cis-monounsaturated
phosphatidylcholine lipid bilayers: a comparison with experiment. J.
Chem. Theory Comput. 6, 325-336</font></p>
<p><font face="Tahoma">A nice site to find coordinates for well
equilibrated lipids is the one of Peter Tieleman<a
href="http://moose.bio.ucalgary.ca/index.php?page=Peter_Tieleman"></a>
(<a class="moz-txt-link-freetext" href="http://moose.bio.ucalgary.ca/">http://moose.bio.ucalgary.ca/</a>).<br>
</font></p>
<p><font face="Tahoma">Good luck with the simulations,<br>
Itamar<br>
</font></p>
<br>
On 6/04/10 9:35 PM, Justin A. Lemkul wrote:
<blockquote cite="mid:4BBB1C77.7080108@vt.edu" type="cite"><br>
<br>
Arun kumar V wrote:
<br>
<blockquote type="cite">Try PRODRG server to build the molecule as
well as to get topology file. Though you might have to be careful in
using this topology file.
<br>
<br>
</blockquote>
<br>
If by "be careful" you mean "don't use this topology," I'll agree :)
The Gromos parameters for lipids (at least Gromos87 and Gromos96 43a1,
given by PRODRG) fall far short of reproducing lipid properties. That,
and the charges assigned by PRODRG for lipids will not resemble any
known parameter set, requiring a complete re-write of this topology.
You could use PRODRG to build the molecule, but there are a number of
other programs that can do that as well (see the Gromacs site for a
list).
<br>
<br>
To the original post: What lipid are you looking to simulate? Many
pre-equilibrated lipid bilayers are available in the public domain,
along with suitable paramters, saving you a lot of work in building
these systems. They can be tricky.
<br>
<br>
-Justin
<br>
<br>
<blockquote type="cite">Arun
<br>
<br>
Saumya wrote:
<br>
<blockquote type="cite">Hi all,
<br>
<br>
Well, I have been trying to make lipid bilayers using genconf of
<br>
gromacs from a single lipid molecule.
<br>
Can anyone tell me how to proceed with the simulation of lipid
<br>
bilayers starting with a single lipid molecule?
<br>
How can I obtain the .pdb file for a lipid?
<br>
Is there any manual that describes the procedure using Gromacs?
<br>
<br>
Hoping for some inputs.
<br>
<br>
Regards
<br>
Saumya
<br>
</blockquote>
<br>
</blockquote>
<br>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@med.monash.edu.au">Itamar.Kass@med.monash.edu.au</a>
============================================</pre>
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