[gmx-users] KALP-15 tutorial

[Roshan Shrestha]

After using this step-
*perl inflategro.pl <http://inflategro.pl> system.gro 4 DPPC 14
system_inflated.gro 5 area.dat*
Reading.....
Scaling lipids....
There are 128 lipids...
with 50 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 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...

Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 26    40
Protein Y-min/max: 25    39
X-range: 14 A    Y-range: 14 A
Building 14 X 14 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 2 nm^2
Area per lipid: 10.4716089904762 nm^2

Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 10.4755772444444 nm^2

Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 10.4716089904762 nm^2

Writing Area per lipid...
Then I updated [ molecules] section of my topol.top as
[ molecules ]
; Compound        #mols
DPPC                126
Protein             1
Then I ran energy minimization. After that I used
*perl inflategro.pl <http://inflategro.pl> EM.gro 0.95 DPPC 0
system_shrink1.gro 5 area_shrink1.dat*
I got,
Reading.....
Scaling lipids....
There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

No protein coordinates found...
Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 10000    -9999
Protein Y-min/max: 10000    -9999
X-range: -19999 A    Y-range: -19999 A
Building -19999 X -19999 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD..
lower TMD..
Area per protein: 0 nm^2
Area per lipid: 0.583197761890625 nm^2

Area per protein, upper half: 0 nm^2
Area per lipid, upper leaflet : 0.583197761890625 nm^2

Area per protein, lower half: 0 nm^2
Area per lipid, lower leaflet : 0.583197761890625 nm^2

Writing Area per lipid...
Done!

*Clearly there is some mistake in here as the Area per protein is 0 and
area per lipid is very low compared to the experimental value.*


-- 
Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal