Unable to read coordinates files of custom molecule about fftool HOT 6 CLOSED

If you start from an xyz file created by a tool such as Avogadro, then you need to edit it to add two things before you can use it with fftool:

1. Provide the name of the file where the force field parameters are to be found (in the second line of the xyz file)
2. Identify the atom types as they are defined in the force field (so each atom will have its partial charge, LJ parameters, bonded terms are found, etc.)
   For TFSI = Ntf2 you can look at the example in the clandp repository.

You'll need a reasonably optimised structure in the xyz, in order for the covalent bonds (topology) to be identified. So you need to check that the number of bonds reported by fftool is correct. If you start from a zmat, then the topology (bonds) is assumed from the 2 first columns (which atoms are bonded to which).

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What software can I use to visualize this zmat format? I tried Avogadro (2), VMD and I have now spent quite some times trying to install molden and webmo without success. I can modify the file by hand but I have several molecules and it'd be great to have an automatic tool.
Thanks

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For xyz files, I need to supply the molecule name and the force field file.
If I don't, the force field will not be recognized (warning: no force field for Li-TFSI) and the mol instance will not have the ffile attribute (spec[i].ffile -> TypeError: unsupported format string passed to NoneType.__format__)

Thus the correct format seems to be this:

16
Li-TFSI    il.ff   #Molecule name and force filed file
CBT        0.86105        0.89295        5.97469
CBT        6.02957        4.09250        5.48800
F1         0.03356        0.14224        5.16180
F1         0.14549        1.94748        6.50829
F1         1.34432        0.09869        6.99662
F1         5.37125        5.30088        5.36485
F1         6.39115        3.89604        6.80688
F1         7.16352        4.10471        4.69862
Li         2.18291        2.36466        8.39555
NBT        3.41917        2.55574        5.86439
OBT        1.78032        2.37959        3.80347
OBT        3.05925        0.41688        4.32394
OBT        4.54153        2.86457        3.47237
OBT        5.62154        1.37603        5.01432
SBT        2.24914        1.53537        4.99852
SBT        4.93368        2.74857        4.95398

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This could help to transcribe xyz -> zmat
https://github.com/robashaw/geomConvert/tree/master

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If you revert back to just chemical element names in the zmat and remove the extra lines with the force field file (and maybe also the 1st column with atom number), then Avogadro should be able to visualise this. The surest way is to comply to the Gaussian z-matrix format.

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In general, you need to be able to edit files quickly and efficiently. Conversion tools stick to "standard" formats and only allow you to go so far.

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