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Shuang Luo

TypeError: 'NoneType' object is not subscriptable

Hello, thank you for uploading this great tool.

I uploaded a pdb file of graphene generated by Material Studio and chose the Dreiding force field.  However,  a 'TypeError' occurs when generating the data file (please see below):

Box size parameters read:
x: 0.000 26.800
y: 0.000 25.550
z: 0.000 70.000
 
Getting information...
Generating DREIDING atom types
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
in run_all(ignore)
     41     print(" ")
     42     print('Getting information...')
---> 43     new_typing_command, data4lammps_command = runData4Lammps.run_data4lammps(charge, infile_is_pdb, boundaries, ffield)
     44     #'Gasteiger'
     45     runCommand(new_typing_command)

~/data/results/1898952/struc2lammpsdf/bin/runData4Lammps.py in run_data4lammps(chargeMethod, infile_is_pdb, boundaries, ffname)
     12         cell_sizes = boundaries
     13         data4lammps_command = 'python2.7 {0} {1} {2} {3} {4} {5} {6} {7} {8} {9} {10}'.format(path, \
---> 14                     cell_sizes[0], cell_sizes[1],\
     15                     cell_sizes[2], cell_sizes[3],\
     16                     cell_sizes[4], cell_sizes[5],\

TypeError: 'NoneType' object is not subscriptable

Can you tell me how to fix this error ?

 

  1. LAMMPS
  2. lammpsdata-file generator
  3. python
  4. tool:struc2lammpsdf
  5. TypeError

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2 Responses

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    Alejandro Strachan

    Try providing a 3D box. So you have a graphene layer within a 3D box.

    I do not think the tool was designed for 2D boxes.

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      Shuang Luo

      Hi Alejandro, 

      Thank you for your reply.  I also tried to convert the sample structure files provided in ./data. The generator works well with a .xyz file or a .cliff file. However, it produces error and can't create Lammps data file when converting a .pdb file.

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    Lorena Alzate-Vargas

    Are you using the latest version of the tool? Also, after it reads the box size you should be able to see if the pdb file was correctly read and converted (it prints number of atoms in the structure and bonds found). It can be a problem with the file formatting you are using.

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      Shuang Luo

      Thank you for your suggestions. I am using the latest online version of the tool. The file I was using is sample_gr_only.pdb. There might be a problem with the pdb file formatting .

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