[gmx-users] protein in membrane

Sweta Iyer iyer at wehi.EDU.AU
Sun Jul 31 05:22:56 CEST 2011


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?!

Cheers
Sweta


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