[gmx-users] vmd does not display the molecule

[leila karami]

dear justin

I checked the VMD mailing list but that does not help me.

first few lines of my gro file :

Protein in water
23136
    1GLY      N    1   1.655   4.898   3.866 -0.3222 -0.2420  0.1437
    1GLY     CA    2   1.677   4.774   3.793  0.0134 -0.2201  0.2050
    1GLY    HA1    3   1.579   4.735   3.767  0.5541 -1.5676  0.1443
    1GLY    HA2    4   1.732   4.708   3.859  1.2946  2.0442  1.5391
    1GLY      C    5   1.760   4.809   3.671  0.1350 -0.3085  0.2633
    1GLY      O    6   1.732   4.904   3.598  0.1431 -0.4147  0.1209
    2SER      N    7   1.867   4.733   3.644  0.3115 -0.0506  0.2274
    2SER      H    8   1.898   4.660   3.706 -1.4080 -0.0311  1.1663
    2SER     CA    9   1.924   4.738   3.511 -0.9271  0.2649 -0.3082
    2SER     HA   10   1.845   4.759   3.439 -0.6670 -0.9431 -0.9674


last few lines of my gro file :

 7208Na      Na23127   1.251   2.111   2.829  0.0512 -0.5390  0.2230
 7209Na      Na23128   0.220   2.894   0.285 -0.0656  0.2288 -0.0477
 7210Na      Na23129   2.803   0.503   5.080  0.0192 -0.1246  0.0370
 7211Na      Na23130   3.718   2.036   1.304 -0.4850 -0.3162  0.4396
 7212Na      Na23131   2.322   3.787   2.485  0.2661  0.1734  0.5773
 7213Na      Na23132   3.592   5.392   5.571  0.4515  0.6877 -0.3284
 7214Na      Na23133   4.708   2.478   0.651 -0.1105  0.1018 -0.4275
 7215Na      Na23134   4.612   4.964   0.340  0.2845 -0.3202  0.0326
 7216Na      Na23135   5.438   6.245   5.071 -0.0165  0.1414 -0.2011
 7217Na      Na23136   5.855   1.272   5.027 -0.3189  0.4687 -0.1455
   6.21600   6.27700   6.26300
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