[gmx-users] Embedding protein into lipid bilayer

[yoochan]

Dear GMX users,

I’m tyring to build lipid and transmembrane(protein) system using inflategro.pl. in GROMACS 5.0.4.

I think the inflategro.pl can not build a result on center of box when the membrane or lipid are quite large.

Here is my workflow

1. Prepare a protein (1R3J)

2. Prepare a optimized DPPC lipid  (dppc128.gro)

3. Make a large DPPC lipid  using editconf command , because 1R3J is bigger than dppc128.gro. (click to show pic <http://technemine.iptime.org:20000/ic/public.php?service=files&t=de809347be67c2f868ff4f51440da78a>)

4. Superimpose a protein and newly prepared DPPC lipids (about 1152 dppc molecules)

5. Run inflategro.pl as below

$ perl inflategro_1.pl prot_memb.nowater.gro 4 DPPC 5 inflated.gro 5 area.dat

6. Check inflated.gro  (click to show pic) <http://technemine.iptime.org:20000/ic/public.php?service=files&t=2f6323524912f91ddc4c3d69fceb7a47>


Any advices?

Many Thanks,

Yoochan