[gmx-users] vmd does not display the molecule

[Erik Marklund]

Erik Marklund skrev:
> leila karami skrev:
>> 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.
> Not sure if it's related, but your topology doesn't match the 
> gro-file. 0 Cl in top, but 1 in gro.
>
> /Erik
Ignore my previous email. I missed that you deleted the Cl-related 
lines. So, did VMD display your system correctly before removing those 
lines?

/Erik

-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys