[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:
> Justin, hello!
> 
> In the algorthm presented in the tutorial there is one inconvenience 
> that is many iterations of the shrinking/minimization of the protein ( 
> e.g if i'd like to obrain good value for S per lipid for my structure). 
> Is there any way to make this process automated ? ( e.g some program 
> wich could do all of those operations untill defined value for some 
> magnitudes would be reached )
> 

Sure, you could do all of it within a shell script that loops the commands and 
checks the printed output.

> Also I'd like to ask about g_membed. As I've understood for that program 
> I need in merged pdb struture ( consist of my peptide inserted in the 
> membrane ) as well as merged topology. Is there any way to prepare this 
> data exept the way presented in your tutorial ? 
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html 
> )
> 

That's what you obtain when concatenating the protein and membrane coordinate 
files in my tutorial, prior to any inflation.  You'd just have to add whatever 
molecules are present in the [molecules] directive of the .top at that point.

> E.g I've heard that this could also be done via PyMol. Where I could 
> find example of such preparation ?
> 

I don't know of one.

-Justin

> 
> Thanks for your help,
> James
> 
> 2011/10/15 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     James Starlight wrote:
> 
>         Dear Gromacs's users!
> 
> 
>         I'd like to simulate some membrane proteins in their native
>         environment.
> 
>         Recently I've found a good tutotial of the same simulation of
>         the KALP peptide in DPPC membrane
>         (http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html>).
> 
>         Is there  someone who have also tried to make thit tutorial ?
> 
> 
>     Yes, per our server logs, several hundred people have :)
> 
> 
>         First of all its very intresting for me the positioning of the
>         protein in the membrane via specific  perl script called
>         infrategro. What values for the cutoff radius as well as
>         measurements of  the area per lipid  are most adequate for
>         different membrane proteins?
> 
> 
>     The ones given in the tutorial work quite well.  They are the
>     defaults suggested by the developers of InflateGRO.
> 
> 
>         Could you also tell me some alternative ways of full algorithm
>         of the protein insertion in the membrane?
> 
> 
> 
>     Careful use of genbox (but will require significantly more
>     equilibration as there will be large gaps), or g_membed.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <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

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