[gmx-users] editconf not centering, and it is cutting off my molecule

[Justin Lemkul]

On 12/31/12 5:50 PM, Xu Dong Huang wrote:
> Dear Justin,
>
> I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning:
>
> star polymer
> 201
>      1star    O4    1   0.000   0.000   0.000
>      1star	 O1	   2   0.430   0.000   0.000
>      1star	 O1	   3   0.860   0.000   0.000
>      1star	 O1	   4   1.290   0.000   0.000
>      1star	 O1	   5   1.720   0.000   0.000
>      1star	 O1	   6   2.150   0.000   0.000
>      1star	 O1	   7   2.580   0.000   0.000
>      1star	 O1	   8   3.010   0.000   0.000
>      1star	 O1    9   3.440   0.000   0.000
>      1star	 O1   10   3.870   0.000   0.000
>      1star	 O1	  11   4.300   0.000   0.000
>      1star	 O1	  12   4.730   0.000   0.000
>      1star	 O1	  13   5.160   0.000   0.000
>      1star	 O1   14   5.590   0.000   0.000
>      1star	 O1   15   6.020   0.000   0.000
>      1star	 O1	  16   6.450   0.000   0.000
>      1star	 O1	  17   6.880   0.000   0.000
>      1star	 O1	  18   7.310   0.000   0.000
>      1star	 O1	  19   7.740   0.000   0.000
>      1star	 O1	  20   8.170   0.000   0.000
> ...
>
> and for the output .gro after editconf, here is what it shows (I don't know why the formats are kind of shifted, )
>
> star polymer
>    201
>      1star    O4    1  11.921  11.921  16.195
>      1star   O1	    2  12.351  11.921  16.195
>      1star   O1	    3  12.781  11.921  16.195
>      1star   O1	    4  13.211  11.921  16.195
>      1star   O1	    5  13.641  11.921  16.195
>      1star   O1	    6  14.071  11.921  16.195
>      1star   O1	    7  14.501  11.921  16.195
>      1star   O1	    8  14.931  11.921  16.195
>      1star    O1    9  15.361  11.921  16.195
>      1star    O1   10  15.791  11.921  16.195
>      1star   O1	   11  16.221  11.921  16.195
>      1star   O1	   12  16.651  11.921  16.195
>      1star   O1	   13  17.081  11.921  16.195
>      1star    O1   14  17.511  11.921  16.195
>      1star    O1   15  17.941  11.921  16.195
> ...
>

The issue here is spacing.  The files have tabs in them, which break the 
mandatory alignment for a .gro file.  The atoms did not display because VMD 
could not correctly read the coordinate fields.

-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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