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

[bhavaniprasad vipperla]

Hi Justin
Could u suggest me which step to carry on further.

In place of inflategro , can we use g_membed.

Regards
Bhavaniprasad

-----Original Message-----

From: Justin Lemkul
Sent: 3 Aug 2012 10:54:49 GMT
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: number of coordinates in coordinate file   (system_inflated.gro,   9331) number of coordinates in coordinate file does not match topology



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
> 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
>

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

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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