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
--
========================================
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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