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structure files with metal(s) in them fails #7

Closed cstein closed 11 years ago

cstein commented 11 years ago

If one uses a file with metal in them, fragit crashes. The problem is that the fragmentation code assumes charges are always available. However, Open Babel silently halts the calculation because of missing charges for the elements.

currently it is now known what the alternative charge-model 'GASTEIGER' does.

it is also unknown how to get the alternative charge-models (http://openbabel.org/dev-api/classOpenBabel_1_1OBChargeModel.shtml#_details) working with the python bindings.

cstein commented 11 years ago

After having tested the proposed charge models (QEQ, QTPIE, EEM, MMFF94 and GASTEIGER) only MMFF94 still appears to work, it is now clear that this is not worth fighting for and we need alternative charge models.

Maybe even load info from a PQR file.