Hi,
Don't know about g_membed. But try to use the method developed by
Tieleman's group
http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis .
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.
Best,
Itamar
On 24/01/11 3:39 PM, Mohana lakshmi wrote:
Dear all
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.....
Thanks and regards
--
Mohanalakshmi N
--
"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
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