[gmx-users] Embedding protein into lipid bilayer

yoochan yuchan.m at gmail.com
Sun Mar 8 13:38:40 CET 2015


Justin Lemkul <jalemkul at ...> writes:

> 
> 
> 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
> 

Thank you for your message.

The picture of preparation process looks weird but I think preparation has done correctly.

The transmembrane region of protein is well located on center of DPPC bilayer.
 
Here, I attach different angle of views about previous picture.

(Top View : https://www.dropbox.com/s/omn1haq3u2psp6v/top.png?dl=0)
(Side View : https://www.dropbox.com/s/9kg05gxi1m0312m/side.png?dl=0)

There is no problem when I run Inflategro.pl with small amounts of DPPC bilayer.

I have no idea about this issue.

Many Thanks,

Yoochan


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