[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:
> Justin,
> 
> Could you tell me what difference in inflategro parameters ( cut-off for 
> lipid removing and scaling factors) should I make for insertion protein 
> in another bilayes in comparison tu tutorial ?
> 

I've never made any changes; it's always worked just fine.

> Now I'm working with DMPC. I've inserted symmetrical alpha helices 
> protein in this bilayer but inflategro deleate 2 lipid from upper and 
> just 1  from lower layer. It's strange because I suppose that equal 
> bilayer molecules would be removed :o
> 

The number of lipids that are removed will depend on the starting configuration 
of the membrane and thus where lipids are relative to the protein. 
Theoretically, a symmetrical protein should delete an equal number of lipids 
from each leaflet, if the geometry of the top and bottom leaflets is comparable. 
  Either try placing the protein at a different location to achieve equivalent 
removal or manually delete a lipid and be sure to equilibrate adequately.

> 
> On Inflategro's sites I havenot found such specifity for above 
> parameters for different bilayers :(

The cutoffs specified are simple grid search parameters.  They do not 
necessarily need to be altered depending upon the lipid type.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================