[gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
jalemkul at vt.edu
Fri Aug 3 12:52:47 CEST 2012
On 8/3/12 12:32 AM, Bhavaniprasad.V wrote:
> 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
> 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...
> So please suggest me what is going wrong
The errors above indicate something is going wrong with printing the output, but
from looking at the code I see no reason why this should come up. It is also
quite possible that no lipids need to be deleted based on the inflated structure.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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