[gmx-users] how to make pdb2gmx to read GLUH

コウ チ caoch_57 at hotmail.com
Thu Sep 9 10:24:56 CEST 2004


hello:
  i used pdb2gmx to creat a .top file which contains GLUH. it seems pdb2gmx 
only read the first three  character codes that i can not creat a 
protonated GLU top file. i have tried to use different format file (ex: 
.gro .g96 .pdb) and every trial failed. 
the .gro file is:
   36
    1GLUH     N    1   1.975  -0.703  -1.325
    1GLUH    CA    2   1.902  -0.600  -1.399
    1GLUH     C    3   1.851  -0.654  -1.532
    1GLUH     O    4   1.741  -0.625  -1.581
    1GLUH    CB    5   1.990  -0.478  -1.426
    1GLUH    CG    6   1.918  -0.366  -1.500
    1GLUH    CD    7   1.813  -0.295  -1.416
    1GLUH   OE1    8   1.792  -0.334  -1.300
    1GLUH   OE2    9   1.751  -0.197  -1.467
    1GLUH     H   10   2.062  -0.695  -1.314
    1GLUH   HE2   11   1.773  -0.189  -1.548
    2ALA     .....
 is there something wrong with this format?how can i resolve it ?
 thank you for help
 regards
                                                                            
       caoch

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