[gmx-users] removal of water from hydrophobic core of lipid

Justin A. Lemkul jalemkul at vt.edu
Tue May 19 15:05:42 CEST 2009

nitu sharma wrote:
>  Dear all
>                  I want remove water molecules from hydrophobic core of 
> lipid by using  script Keepbyz.pl by (chris neale) . I want to know  
> basis of deciding uprez and lowrez variables . I mean to say how can I 
> decide which value of uprez and lowrez is suitable for my system protein 
> embedded in lipid bilayer.

The bounds of the hydrophobic core (i.e., the start of the acyl chains) are 
probably a reasonable place to start.


> If anyone did these things please help me in solving this problem.
> I will be really thankful for that.
> Nitu Sharma
> School of Life Sciences
> Jawaherlal Nehru University
> New delhi , India
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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