[gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

[Bhavaniprasad.V]

hi justin,

the problem is actually InflateGro is not deleting any lipids.
I had inserted the protein in lipid using VMD and saved the coordinate file and
using that directly to this step

cat pro_in_pope.gro pope_whole.gro > system.gro

after running perl inflategro.pl system.gro 4 POPE 14 system_inflated.gro 5
area.dat.
Argument "P8" isn't numeric in printf at inflategro.pl line 708.
Argument "O9" isn't numeric in printf at inflategro.pl line 708.

Calculating Area per lipid...
Protein X-min/max: -4    103
Protein Y-min/max: -14    100
X-range: 107 A    Y-range: 114 A
Building 107 X 114 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 107.75 nm^2
Area per lipid: 8.02906194817911 nm^2

Area per protein, upper half: 101.25 nm^2
Area per lipid, upper leaflet : 8.09202321149701 nm^2

Area per protein, lower half: 102.25 nm^2
Area per lipid, lower leaflet : 8.03790402571429 nm^2

Writing Area per lipid...
Done!

So please suggest me what is going wrong

Regards
bhavani