On 9/21/12 11:16 AM, Shima Arasteh wrote:
Dear users and admins,
I'm trying to use GridMAT to get the area per lipid and thickness.
To do so I ran this command:
# perl GridMAT-MD.pl param_example
It doesn't give me any valuable output. This error comes out:
Generating the grid...
Your system is bigger in the X-direction
There are 20 grid points in the X direction, spaced every 0.470368421052632
nanometers
There are 19 grid points in the Y direction, spaced every 0.480833333333333
nanometers
Note: the intervals may not be exactly the same in order to have a whole number
of grid points
Analyzing the bilayer...
The top leaflet "thickness" will be printed to 20x19_top_pbc.dat
The bottom leaflet "thickness" will be printed to 20x19_bottom_pbc.dat
The average bilayer "thickness" will be printed to 20x19_average_pbc.dat
Calculating area per lipid head group...
Illegal division by zero at GridMAT-MD.pl line 587.
Would you help me please to get the desired results?
This usually means the atom or residue naming is wrong, the formatting is wrong,
or some other obscure problem. Email me (off-list) your input file and
coordinate file and I will take a look, since this isn't really a Gromacs issue.
-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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