[gmx-users] InflateGRO and pentamer protein simulation

[xi zhao]

Dear sir :
I want to a pentamer membrane protein, when I used InflateGRO.pl with DOUGHNUT Mode, the results were wrong, please help me! 
show " [user at localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits
Doughnut mode activated. Protein coordinates will be translated by subunit ....
Reading..... 
Reading chain identifiers.... 
Subunit 1:  atom 1 to  atom 3238 
Subunit 2:  atom 3239 to  atom 6476 
Subunit 3:  atom 6477 to  atom 9714 
Subunit 4:  atom 9715 to  atom 12952 
Subunit 5:  atom 12953 to  atom 16190 
There are 5 protein subunits.... 
Scaling lipids....
There are 512 lipids...
with 65 atoms per lipid..
Determining upper and lower leaflet...
256 lipids in the upper...
256 lipids in the lower leaflet 
Checking for overlap....
...this might actually take a while...
.......
Argument "N4" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "C5" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "C6" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "O7" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "P8" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "O9" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "A1" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "A2" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "C1" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "C2" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "C3" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "N4" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "C5" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "C6" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "O7" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "P8" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "O9" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "A1" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Argument "A2" isn't numeric in printf at inflategro.txt line 708, <CHAINS> line 5.
Calculating Area per lipid...
Protein X-min/max: 23    105
Protein Y-min/max: 18    100
X-range: 82 A    Y-range: 82 A
Building 82 X 82 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 49 nm^2
Area per lipid: 9.83158146861789 nm^2
Area per protein, upper half: 38.75 nm^2
Area per lipid, upper leaflet : 9.79362516645161 nm^2
Area per protein, lower half: 45.75 nm^2
Area per lipid, lower leaflet : 9.92548787409836 nm^2
Writing Area per lipid...
Done!


      
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