[gmx-users] About Packaging of Protein by Lipids

vidhya sankar scvsankar_agr at yahoo.com
Thu Oct 25 17:40:02 CEST 2012

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)  

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

Thanks In Advance

More information about the gromacs.org_gmx-users mailing list