[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 17 13:31:25 CEST 2011

James Starlight wrote:
> Justin
>     Sure, you could do all of it within a shell script that loops the
>     commands and checks the printed output.
> As I understood in that iterations only step with scalling by factor 
> 0.95 and futher energy minimization must be included until desired S per 
> lipid will be reached. Could you provide me with a small example of such 
> script for better understanding of the syntax. I've never done unix's 
> shell scripts before :)

I don't have one on hand, sorry.  An hour or so spent with shell scripting 
tutorials will probably lead you to it, though.

> Could you tell me where I could found experimental valuee for Area per 
> lipid for differen cases (e.g I'll be work with large membrane proteins 
> such as membrane receptors so i wounder to know what values of S per 
> lipid as well as S per protein I might expect in that case)

Some are given in the tutorial, along with references.  If you're a lipid that's 
not listed, you'll have to find such information in the literature.

> Also I have a question about solvation of my membrane protein via 
> GENBOX. I found 2 possible ways to exclude water from the insertion into 
> membrane
> - Changing vdv radii for the C atoms- So i've copied  vdwradii.dat to my 
> work dirrectory and changed vdv R. How I should to define that genbox 
> uses exactly that modified file located in my working directory instead 
> of default vdwradii.dat? Finally how I can check that there are not 
> waters within the membrane ? (I've tried to visualize via VMD but the 
> overal picture is very unclear :) )

The working directory is always searched first.  This is true for all Gromacs 
programs.  Visualization is the only way to tell.  Perhaps you need to render a 
more clear image.  Simply loading the .gro file and not making any refinements 
to the representation is a good way to go cross-eyed :)

> - Also I've found that I can Running short md to exclude those waters 
> via hyfrophobic effect.  What parametries would be opti,al for that 
> simulation in case of KALP as well as other more larger proteins ?

The same parameters that you would use to run normal MD on such a system; 
there's nothing special about this procedure.  Restraints would be advisable.


> Thank you for your help,
> James


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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