[gmx-users] protein embedded into membrane.

[Justin A. Lemkul]

#ZHAO LINA# wrote:
> 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?
> 

Area per lipid will equilibrate with sufficient simulation.  Otherwise, use 
normal EM criteria to determine whether or not your system is in a reasonable 
configuration.

-Justin

> Thanks and best regards,
> 
> lina 
> 
> ________________________________________
> 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.
> 
> -Justin
> 
>> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================