[gmx-users] protein embedded into membrane.

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 4 17:27:45 CEST 2010

#ZHAO LINA# wrote:
> Hi,
> When I tried to pack different proteins around the lipids (this protein 
> I put it in the position which was nearly going to jump out of the 
> lipids, so it's not exactly inserted into it, just very shallow into 
> it), I used the vmd to see the system.gro, which without being inflated 
> first, I noticed
> some warnings like this:
> Warning) Unusual bond between residues:  40 (protein) and 491 (none)
> Warning) Unusual bond between residues:  40 (protein) and 491 (none)
> Warning) Unusual bond between residues:  40 (protein) and 491 (none)
> when I removed those residues such as 491 (none), not protein ones, 
> those warning disappeared.

VMD is detecting close contacts, not actual bonds, but since its heuristic 
algorithm tells it there are bonds, then you get these warnings.  Perhaps a 
simple EM will resolve them, but maybe not.

> I noticed on Justine's tutorial, there were 26 iterations of scaling 
> down. I did those iterations step by step manually before and cost me 
> nearly 40 mind-not-running minutes to finish, but later I spent crazy 2 
> hours or more to write a short and clumsy script to save mine 40 mins 
> work in the future. This is not the point.  The point was that, are 
> there some shortcuts? I wonder whether I could avoid doing those 
> inflategro first, and then shrink and energy minimization also being 
> avoided by simply removed those lipids (I know I still need a final EM).
> or,

What is presented in the tutorial is simply one way to build a membrane protein 
system.  If you have an easier case, then as long as you can justify your 
methods, do what you see fit.  Perhaps the iterations of InflateGRO are, in your 
case, unnecessary.  There is also a new tool called g_membed that might be 
useful.  It is far more automated than InflateGRO, but I have never used it myself.

> Can we locally inflated those membrane and then locally packed them 
> together. Very local, or maybe just simply removed those lipids.

Not to my knowledge, unless you write this program yourself.

> How could I make sure the removal ones are going to be nice, from which 
> sides I should check.

I don't understand what you're asking for here.


> Thanks and best regards,
> lina
> p.s  To avoid a very trivial description, I put some background 
> information below, thanks for your time.
> from Tieleman's website
> http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis
> and Justine's webpage
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
>  I tried pack the lipids around the protein, no doubt followed perfectly 
> based on the tutorial before.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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