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Hi,<br>
<br>
Don't know about g_membed. But try to use the method developed by
Tieleman's group
<a class="moz-txt-link-freetext" href="http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis">http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis</a> .<br>
<br>
Or use the old method of taking a n equilibrated membrane with a
protein, take it out and stuck yours. Just do long PR simulation. <br>
<br>
Best,<br>
Itamar<br>
<br>
<br>
On 24/01/11 3:39 PM, Mohana lakshmi wrote:
<blockquote
cite="mid:AANLkTim9frpKqa0OG8h-mTSKa=DmS6NOExq6-9m8nGsx@mail.gmail.com"
type="cite">Dear all<br>
<br>
I am trying to run simulation of transmembrane protein, i am
looking for better ways to setup protein with lipid membrane.
initially i used VMD to insert protein with lipid membrane but it
did not come out well, i got errors while running position
restraint. i read about g_membed tool in gromacs, is it helpful
for setting up transmembrane proteins also? Is there any other
better ways to insert protein perfectly into the membrane? Please
help me to overcome this problem.....<br>
<br>
<br>
<br>
Thanks and regards<br>
-- <br>
<br>
<br>
Mohanalakshmi N<input type="hidden"><input type="hidden"><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@monash.edu">Itamar.Kass@monash.edu</a>
============================================</pre>
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