[gmx-users] RE: Insertion of protein in lipid bilayer

rob yang nextgame at hotmail.com
Thu Aug 4 20:38:10 CEST 2005

Thank you Dr. G, Smith. I fixed the problem in lipids jumping around, and 
was able to obtain 1 ns of md (make_hole version) for the membrane with the 
hole alone. The membrane seemed to be stable as the bilayer stayed where 
they were supposed to this time and boy did I ever enjoy the trajectory 
movie. However, upon further inspection, the hole had "sealed up" at the end 
of the simulation.  The hole I created using the make_hole.pl before running 
the md had been filled by surrounding lipids. This led me to think that 
maybe the exclusion forces of the protein surface are not correct (could be 
due to user error on my part when using MSMS?). I examined the 
insidesurf.pdb and molsurfpdb.pdb using vmd and couldn't figure out what I 
should be looking for.

So my questions are:
1) How can I use the information of insidsurf.pdb and molsurfpdb.pdb (maybe 
perhaps gsurf.log) to convince myself that the calculated forces are indeed 
"reasonable".  In the tutorial it says that the forces of the insidesurf.pdb 
should be pointing outward at the right residues, but I couldn't see any 
directions.  I.e, what would be a sanity test here?
2) Any other reasons why the hole grew back together?

thanks alot

>From: "Graham Smith" <graham.smith at biiuk.com>
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>Subject: [gmx-users] RE:  Insertion of protein in lipid bilayer Date: Tue, 
>2 Aug 2005 21:40:23 +0100
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> > I did follow the position restraint step in my run by restricting P8
>in the
> > z direction. What happened was that the 2 popc layers flipped right
>off the
> > bat in the md so that the head groups and water from each layer were
> > each other while the hydrophobic tails from each layer were situated
>as far
> > away from each other as possible. It was really quite bizzare and
> > getting a few chuckles from it, I'd like to find out what I did wrong.
> > is what I did:
> > 1) got the 128 popc pdb and itp from Sir Tieleman, used
> >
> > forcefields
>I think they haven't "really" done that, you've probably got an illusion
>due to periodic boundary conditions (sketch your system replicated along
>z and you'll see what I mean). The simulation you've got isn't wrong but
>you may want to change the coord file and repeat it so things look more
>normal. See note (c) below ...
> > 2) followed the how-to html to create holes using msms.
> > A few questions here:
> > a) should I minimize the new membrane with hole?
>It won't do any harm, but it might well work without it anyway.
> > b) how critical is removing all the possible lipids that may clash
>with the
> > protein?
>Not at all. The whole idea is that it will push the remaining ones out.
> > c) I simply used vmd to manually put my proteins into the membrane
>lipid and
> > saved the coordinate of the protein in a seperate file. Then I copied
> > pasted the simulation box size from the membrane  pdb file to the top
>of my
> > protein file. Is this acceptable? What would be the most bullet-proof
> > approach?
>Moving files around with vmd could perhaps be the source of the apparent
>"flipping" of the lipids - e.g. if it has centered something at (0,0,0);
>gromacs avoids -ve coordinates and wraps them round into the next
>periodic image. I generally use editconf -center [rvec] or editconf -c
>to move things around, then subsequently concatenate the pdb files and
>view the result to check I've got it right.
> > 3) grompp and mdrun using the following parameters.
> > run.mdp
> > A few questions here too:
> > a) what would typical values be for the tau_p and tau_t?
>I use tau-t = 0.1 and tau-p = 1.0 with Berendsen coupling but I don't
>think it's critical, especially in an unphysical simulation like this.
> > 4) I havn't got to this step yet but after the hole has been generated
> > successfully generated in the membrane, do I append the protein.pdb
>file to
> > the end of the membrane_hole.pdb file and run a normal em/md to the
>Yes. Well, I normally put the protein first, but the order of the
>components (protein, lipid, water, ions if you have them) doesn't
>matter, as long as they're the same in the pdb file and the topology.
>Dr Graham R. Smith
>Biosystems Informatics Institute
>Newcastle upon Tyne NE1 4EP
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