[gmx-users] About Packaging of Protein by Lipids

Justin Lemkul jalemkul at vt.edu
Thu Oct 25 17:43:46 CEST 2012

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 ?


> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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