[gmx-users] vmd does not display the molecule

[Justin A. Lemkul]

leila karami wrote:
> dear justin
>  
> I checked the VMD mailing list but that does not help me.
>  
> first few lines of my gro file :
>  

Well, the structure of the .gro file appears intact.  Somewhere along the way, 
VMD thinks it's hitting the end of the file.  Have you manipulated or edited the 
file in any way?  Opened it using some weird Windows software that saved some 
hidden characters or something?  If so, you can run it through dos2unix to 
correct that.

As an aside, what kind of model are you using?  You have explicit HA atoms on 
the CA of GLY (OPLS? AMBER?), but no N-terminal protonation.  That would seem to 
be a completely fictitious and unreasonable model for a standard N-terminal 
glycine.  Not related to your problem, but I seem to be on a roll of free advice 
this morning :)

-Justin

> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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