[gmx-users] About Packaging of Protein by Lipids

[Justin Lemkul]

On 10/25/12 11:40 AM, vidhya sankar wrote:
> Dear Justin Thank you for your Previous reply,
>                                                                                  But When I use Vandewalls Radii for Carbon Atom 0.375 As Quoted in your tutorial  Then My Protein-Lipid System is solvated with 22000 Water Molecules  Most of them are Within  Bilayer .  This is Huge number  I Think
>
> From  your reply Mail I came  to Conclusion  that I need to  Pack Lipid effectively Around Protein using
> inflategro .pl script   (By doing More number of iterations Than I did Before  )  Thereby I can Eliminate  Presence of Void In my system
>
> Is My  Above Understanding   is correct or Not ?
>

Yes.

> Also When I do the more Iteration using  inflategro.pl  script
>
> My  area per lipid Is very less than Experimental value for DPPC lipid (62 A)
>

InflateGRO overestimates the APL value, so your DPPC are probably very 
over-compressed at this point.

> Then  Can  i continue My solvation    with this  Low area ( I am using Box size of 6 6 6 )
>

I'm not going to try to blindly judge whether or not that will work.  You know 
what you need to do.  Try it and see.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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