[gmx-users] Embedding protein into lipid bilayer

[Justin Lemkul]

On 3/6/15 11:02 PM, yoochan wrote:
> 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.
>

That's not likely true.

> 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>
>

This image suggests that you haven't prepared the system correctly (either step 
3 or 4, or both).  If the protein is off-center from the lipids, that comes from 
incorrect initial placement.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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