[gmx-users] protein embedded into membrane.

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Mon Oct 4 17:42:06 CEST 2010

Thanks for your answering. I will check those further later.

The unclear question was that, to the final .gro. How can I tell it that one (protein embedded in membrane) is okay or nice, so I can continue.

based on area per lipids, or after EM ... are there some criteria?

Thanks and best regards,


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Monday, October 04, 2010 11:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] protein embedded into membrane.

#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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