[gmx-users] About Packaging of Protein by Lipids
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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