[gmx-users] perfluorohexane pdb

[jalemkul at vt.edu]

Quoting ABEL Stephane 175950 <Stephane.ABEL at cea.fr>:

> Re hi Marcelo,
>
> Below the perfluorohexane molecule in the pdb format construct with  
> the Discovery Studio Visualizer v2.5
>
> REMARK   Accelrys Discovery Studio PDB file
> REMARK   Created:  Mon Jan 10 20:52:13 Paris, Madrid 2011
> HETATM    1  C1          0     -11.336  -0.581   0.212  1.00  0.00    
>         C
> HETATM    2  C2          0     -10.035  -0.174  -0.542  1.00  0.00    
>         C
> HETATM    3  C3          0      -8.771  -0.197   0.410  1.00  0.00    
>         C
> HETATM    4  C4          0      -7.458   0.219  -0.369  1.00  0.00    
>         C
> HETATM    5  C5          0      -6.194   0.196   0.583  1.00  0.00    
>         C
> HETATM    6  C6          0      -4.893   0.603  -0.171  1.00  0.00    
>         C
> HETATM    7  F7          0     -11.590   0.293   1.248  1.00  0.00    
>         F
> HETATM    8  F8          0     -11.226  -1.862   0.712  1.00  0.00    
>         F
> HETATM    9  F9          0     -12.391  -0.539  -0.675  1.00  0.00    
>         F
> HETATM   10  F10         0     -10.216   1.097  -1.046  1.00  0.00    
>         F
> HETATM   11  F11         0      -9.852  -1.059  -1.582  1.00  0.00    
>         F
> HETATM   12  F12         0      -8.977   0.685   1.449  1.00  0.00    
>         F
> HETATM   13  F13         0      -8.613  -1.470   0.913  1.00  0.00    
>         F
> HETATM   14  F14         0      -7.617   1.493  -0.871  1.00  0.00    
>         F
> HETATM   15  F15         0      -7.252  -0.663  -1.408  1.00  0.00    
>         F
> HETATM   16  F16         0      -6.377   1.082   1.623  1.00  0.00    
>         F
> HETATM   17  F17         0      -6.013  -1.074   1.087  1.00  0.00    
>         F
> HETATM   18  F18         0      -5.004   1.884  -0.671  1.00  0.00    
>         F
> HETATM   19  F19         0      -4.639  -0.271  -1.207  1.00  0.00    
>         F
> HETATM   20  F20         0      -3.839   0.561   0.716  1.00  0.00    
>         F
> END
>
> The structure needs some changes (atom names ?) and minimization  
> steps to relax the structure.
>

If you want Gromacs to read this file, it also needs residue names.   
PDB format is fixed, and this set of coordinates is not correctly  
formatted, so it will undoubtedly cause problems in Gromacs.

-Justin

> hope this helps
>
> Stephane
>
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