[gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/7/18 3:07 AM, negar habibzadeh wrote:
> I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
> your tutorial  When I use inflategro script For my System I have got
> Output System_inflated.gro file with certain message in Command prompt
> as follows  . The Below Message Shows That There is No Lipid Molecules
> Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
> the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
> Molecules Need to be Deleted ?

Maybe there just aren't any lipids overlapping with the protein; that 
can happen.

-Justin

> There are 128 lipids...
> with 138 atoms per lipid..
>
> Determining upper and lower leaflet...
> 64 lipids in the upper...
> 64 lipids in the lower leaflet
>
> Centering protein....
> Checking for overlap....
> ...this might actually take a while....
> 100 % done...
> There are 0 lipids within cut-off range...
> 0 will be removed from the upper leaflet...
> 0 will be removed from the lower leaflet...
>
> Writing scaled bilayer & centered protein...
>
>
> Calculating Area per lipid...
> Protein X-min/max: 24    41
> Protein Y-min/max: 23    43
> X-range: 17 A    Y-range: 20 A
> Building 17 X 20 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD....
> lower TMD....
> Area per protein: 3.25 nm^2
> Area per lipid: 10.7582741393 nm^2
>
> Area per protein, upper half: 2.25 nm^2
> Area per lipid, upper leaflet : 10.7738991393 nm^2
>
> Area per protein, lower half: 2.5 nm^2
> Area per lipid, lower leaflet : 10.7699928893 nm^2
>
> Writing Area per lipid...
> Done!

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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