User 677b9c22ff
07-10-2010 17:26:26
Hi,
tried to calculate pka or microdistribution for
[H]OC(=O)C([H])(N([H])[H])C([H])(OP(=O)(O[H])O[H])C([H])([H])[H]
InChIKey=USRGIUJOYOXOQJ-UHFFFAOYAF
but got the error in Marvin 5.3.8: "Cannot run plugin: pKa - Array index out of range: 14"
java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 14
at chemaxon.struc.MoleculeGraph.getAtom(Unknown Source)
at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Unknown Source)
at chemaxon.marvin.modules.Hydrogenize.callback(Unknown Source)
at chemaxon.struc.Molecule.callHydrogenize(Unknown Source)
at chemaxon.struc.MoleculeGraph.callHydrogenize(Unknown Source)
at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(Unknown Source)
at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(Unknown Source)
at chemaxon.marvin.calculations.pKaPlugin.standardize(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPlugin.createStandardizedMolecule(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.callback(Unknown Source)
at chemaxon.marvin.plugin.PluginManager.callback(Unknown Source)
at chemaxon.marvin.common.swing.MolPanel$5.run(Unknown Source)
Works fine in MarvinView 5.3.2 (I used the 5.3.8 via webstart and LICs seem fine, otherwise a LIC error would show up)
14 (?) What is the progam telling me? The new universal answer to everything :-)
See Wolfram Alpha:
http://www.wolframalpha.com/input/?i=Universal+Answer+to+everything+
Tobias
ChemAxon e08c317633
11-10-2010 12:00:08
Hi Tobias,
TobiasKind wrote: |
Hi,
tried to calculate pka or microdistribution for
[H]OC(=O)C([H])(N([H])[H])C([H])(OP(=O)(O[H])O[H])C([H])([H])[H]
InChIKey=USRGIUJOYOXOQJ-UHFFFAOYAF
but got the error in Marvin 5.3.8: "Cannot run plugin: pKa - Array index out of range: 14"
java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 14
at chemaxon.struc.MoleculeGraph.getAtom(Unknown Source)
at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Unknown Source)
at chemaxon.marvin.modules.Hydrogenize.callback(Unknown Source)
at chemaxon.struc.Molecule.callHydrogenize(Unknown Source)
at chemaxon.struc.MoleculeGraph.callHydrogenize(Unknown Source)
at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(Unknown Source)
at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(Unknown Source)
at chemaxon.marvin.calculations.pKaPlugin.standardize(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPlugin.createStandardizedMolecule(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(Unknown Source)
at chemaxon.marvin.plugin.CalculatorPluginManager.callback(Unknown Source)
at chemaxon.marvin.plugin.PluginManager.callback(Unknown Source)
at chemaxon.marvin.common.swing.MolPanel$5.run(Unknown Source)
Works fine in MarvinView 5.3.2 (I used the 5.3.8 via webstart and LICs seem fine, otherwise a LIC error would show up)
|
It will be fixed in Marvin 5.4.
Workaround: remove the explicit hydrogens ("Structure->Remove->Remove Explicit Hydrogens") before the pKa calculation.
Sorry for the inconvenience.
14 is the atom index. Maybe we will consider to implement a calculator plugin which can tell the universal answer to everything ;-)
Zsolt