On 8/3/12 10:52 AM, bhavaniprasad vipperla wrote:
Hi Justin
Could u suggest me which step to carry on further.
It's not clear to me that InflateGRO truly failed, though some of the output is
curious, as noted before.
In place of inflategro , can we use g_membed.
Sure. I don't use it personally, but others do.
-Justin
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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========================================
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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