[gmx-users] protein embedded into membrane.

[#ZHAO LINA#]

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.

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

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

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.


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