[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:
> 
> James,
> 
> As the consequence the correct orientation of the peptide in the 
> membrane as well as futher solvation are caused many questions :)
> 
> 
> Firsly, following by tutorial guide I've done orientation of KALP 
> peptide in the membrane by
> 
> 1- perl inflategro.pl <http://inflategro.pl/> confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> 2- minimization
> 3- perl inflategro.pl <http://inflategro.pl/> system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
> 
> 
> 
> 4- minimization
> 
> after six iterations of the  3rd and 4th steps I've obtained 6,5 nm^2 value for the area per lipid
> 

The tutorial suggests at least 26 or so iterations.  Your APL value is 100 times 
larger than it should be.

> Next I've done solvation of my protein ( including big vdv radii for carbons )
> 
> 
> 
> Finally my sytem is consisted of 70000 atoms. I think that it's too big ammount of water molecules for such small protein like KALP
> 

Yes, because your membrane is not correctly packed.

> so its seems that i've done some mistakes-
> 1- During shrinking of my peptide- I think that obtained structure (http://www.sendspace.com/file/wenkf4) consist of too big distances beetween peptides so it should be futher shrinked.
> 

Correct.

> 
> 
> But how many iterations must be? I've found in the tutorial that 65 A^2 is good value for that system. But maybe I've used wrong parametries in the pl program?
> 

No, you just haven't done enough iterations.  See above.  Your value is 6.5 nm^2 
, which is 6500 A^2.

> 2- Or maybe too many waters are moved within the membrane in spite of increased VDV radius for carbon atoms. So what I should do for the excluding all unnecessary water from my structure?
> 
> 

Ignore this for now.  Your system simply isn't built correctly.

> 
> E.g I want to simulate hydrophobic effect. What length of that simulation must be ?

Perhaps tens of ns.

> How I can evaluate the ammount of water before and after simulations?

Visualization.

> Finally, What other options of Genbox could I use for preventing insertion of water into my membrane ?
> 
> 

None.  A better starting model is required.

-Justin

-- 
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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

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