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#124 Partial Charges

closed
nobody
None
5
2007-07-25
2007-06-27
Anonymous
No

After create a Gaussian output file with a program called WebMO, Jmol should be able to read it and display the partial charges of the molecule. It does not currently do this. Nor does it do this with files created using MOPAC or GAMESS. Although the files contain the necessary information, for some reason Jmol does not display the charges. When I make an attempt to show the partials, they just come as 0.0. If this could be fixed it would be great. I have yet to find a file format that works with this.

Discussion

  • water molecule created in WebMO using Gaussian

     
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  • Rene Kanters
    Rene Kanters
    2007-06-27

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    Your file has two models in it because structural information is present from the 'input orientation' and the 'standard orientation'. When the charge information is encountered it is only associated with the last atomset read, which in this case is the second one.
    If you pick model number 2 from the list of models in the popup, you'll see that the charges are indeed associated with that one.

     
  • Logged In: NO

    Jmol reads partial charges from the following file types:

    chem3d
    cml
    Gaussian output
    PDB
    CSF
    ghemical
    hin
    mol2
    mopac2007
    mopac93,97,2002
    nwchem
    pqr
    qchem
    spartan

    Is it possible you are not realizing that the partial charges are not always associated with ALL models in a model set? So, for example, in Gaussian files they are typically associated with the second frame, not the first. Same as orbitals.

    Bob Hanson

     
  • Bob Hanson
    Bob Hanson
    2007-07-25

    • status: open --> closed