[gmx-users] transmembrane protein simulation

[Itamar Kass]

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
| E-mail: Itamar.Kass at monash.edu
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