[gmx-users] protein in membrane

[Justin A. Lemkul]

Sweta Iyer wrote:
> Hi,
> 
> I used the inflategro.pl script to insert my protein into the membrane and
> scaled down the lipids until it reached the recommended area per lipid
> value. After removing 4 lipid molecules, I started with an area of 90
> square angstrom and reached a value of 65 square angstrom within just 5
> iterations. However, when I had a look at my gro file, all my lipids look
> spaced out and there seems to be too much of gap between the lipids and
> the protein such that if I solvate it, I am pretty sure water molecules
> can easily occupy those cavities.
> 
> I am wondering what would have possibly gone wrong?!
> 

Probably in unit conversion, but without knowing the initial inflation factor, 
it's hard to say for sure, but if you only reached 90 A^2 in the initial 
inflation I'd suspect you'd have a ton more lipids removed, even for a very 
small protein.  Did you multiply the InflateGRO output by 10 or 100?  The latter 
is correct to convert between nm^2 and A^2 (1 nm^2 = 100 A^2).  You can always 
check progress using box vectors; if they are not close to the original membrane 
structure, you're not done.

-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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