[gmx-users] vmd does not display the molecule

[leila karami]

dear justin

I transfer gro files from linux to windows through SSH secure shell program.
I added 10 Na ions by genion command but in gro file following case is
appeared:

7208Na      Na23127   1.533   2.176   2.687  0.1841 -0.1829 -0.2991
 7209Na      Na23128   0.179   2.821   0.336 -0.2683 -0.1820  0.5803
 7210Na      Na23129   2.288   0.458   4.819 -0.1171  0.7612 -0.4903
 7211Na      Na23130   3.640   1.815   1.138 -0.1083 -0.1591  0.0485
 7212Na      Na23131   2.183   3.845   1.964 -0.0409 -0.1492  0.6725
 7213Na      Na23132   3.356   5.216   5.834 -0.2686  0.1059 -0.1660
 7214Na      Na23133   4.304   2.510   0.809 -0.2994  0.3939  0.7264
 7215Na      Na23134   4.609   4.931   0.535 -0.2609  0.1315 -0.1767
 7216Na      Na23135   5.553   6.022   5.152  0.3516 -0.2021  0.2022
 7217Na      Na23136   5.865   1.114   5.034  0.0442  0.0272  0.3437
*7218Cl        Cl23137    0.000   0.000   0.000  0.0000   0.0000 0.0000
*   6.15463   6.21503   6.20117

I deleted line of        7218Cl        Cl23137    0.000   0.000
0.000  0.0000   0.0000 0.0000

in top file following case is appeared:
[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
SOL         7117
Na          10
Cl          0

I deleted last line.

I am using amber03 force field in gromacs program to study interaction of
pr-dna.
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