Force field conversion errors

Hi,

I got a couple of errors during force field 3D cleaning with molconvert 6.0.5

First error: java.lang.RuntimeException: Rank mismatch

Second error: java.lang.UnsUnsupportedOperationException: Rethrow Rethrow Rethrow Rethrow 

The data source as SDF is here: pkuxxj.pku.edu.cn/UNPD/download.php

Command called: molconvert -m sdf:+H  -3:S{fine} input.sdf

Tobias

          at chemaxon.calculations.clean.Clean3D.modfunc_0(Clean3D.java:858)

        at chemaxon.calculations.clean.Clean3D.optimization3D(Clean3D.java:361)

        at chemaxon.calculations.clean.Cleaner.cleanMolGraph(Cleaner.java:247)

        at chemaxon.calculations.clean.Cleaner.cleanMol(Cleaner.java:311)

        at chemaxon.calculations.clean.Cleaner.clean(Cleaner.java:64)

        at chemaxon.calculations.clean.CleanerUtil.clean(CleanerUtil.java:28)

        at chemaxon.struc.MoleculeGraph.clean(Unknown Source)

        at chemaxon.struc.MoleculeGraph.clean(Unknown Source)

        at chemaxon.formats.MolConverter.convert0(MolConverter.java:1058)

        at chemaxon.formats.MolConverter.convert(MolConverter.java:850)

        at chemaxon.formats.MolConverter.main(MolConverter.java:2010)

Optimizer exception: Rank mismatch

java.lang.RuntimeException: Rank mismatch

        at chemaxon.marvin.modelling.linalg.GradientOptimization.multiDimensionalSearch(GradientOptimization.java:866)

        at chemaxon.marvin.modelling.linalg.GradientOptimization.multiDimensionalSearch(GradientOptimization.java:726)

        at chemaxon.marvin.modelling.linalg.GradientOptimization.doStep(GradientOptimization.java:512)

        at chemaxon.marvin.modelling.linalg.GradientOptimization.run(GradientOptimization.java:390)

        at chemaxon.marvin.modelling.struc.Fragment.invokeNewOptim(Fragment.java:838)

        at chemaxon.marvin.modelling.struc.Fragment.optimizeForcefield(Fragment.java:1075)

        at chemaxon.marvin.modelling.build.fafuse.FuseBuilder.makeCoords2_0(FuseBuilder.java:907)

        at chemaxon.marvin.modelling.build.fafuse.FuseBuilder.makeCoords2(FuseBuilder.java:298)

as well as this one, 

Exception in Clean3D. Failed structure:

java.lang.UnsUnsupportedOperationException: Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow Rethrow null

        at chemaxon.marvin.modelling.build.FragFragFuseBuildCommand.invokeBuild(FragFragFuseBuildCommand.java:248)

        at chemaxon.marvin.modelling.build.BuildCommandBase.callInvokeBuild(BuildCommandBase.java:631)

        at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:383)

        at chemaxon.marvin.modelling.build.BuildCommandBase.build(BuildCommandBase.java:987)

        at chemaxon.marvin.modelling.build.FragClean.startCleanOnSingleFragment(FragClean.java:194)

        at chemaxon.marvin.modelling.interfacing.InvokeFFFBuildCalculation.invoke(InvokeFFFBuildCalculation.java:38)

        at chemaxon.marvin.modelling.interfacing.MultifragMoleculeAdapter.invoke(MultifragMoleculeAdapter.java:46)

        at chemaxon.marvin.modelling.interfacing.CxnMoleculeAdapter.invoke(CxnMoleculeAdapter.java:47)

        at chemaxon.marvin.modelling.interfacing.InvokeCalculation.invoke(InvokeCalculation.java:23)

        at chemaxon.calculations.clean.Clean3D.modfunc_0(Clean3D.java:858)

        at chemaxon.calculations.clean.Clean3D.optimization3D(Clean3D.java:361)

        at chemaxon.calculations.clean.Cleaner.cleanMolGraph(Cleaner.java:247)

        at chemaxon.calculations.clean.Cleaner.cleanMol(Cleaner.java:311)

        at chemaxon.calculations.clean.Cleaner.clean(Cleaner.java:64)

        at chemaxon.calculations.clean.CleanerUtil.clean(CleanerUtil.java:28)

        at chemaxon.formats.MolExporter.clean(MolExporter.java:1397)

        at chemaxon.formats.MolExporter.write(MolExporter.java:781)

        at chemaxon.formats.MolConverter.write(MolConverter.java:1214)

        at chemaxon.formats.MolConverter.convert0(MolConverter.java:1087)

        at chemaxon.formats.MolConverter.convert(MolConverter.java:850)

        at chemaxon.formats.MolConverter.main(MolConverter.java:2010)

 

Cheers

Tobias

Hi,

We are investigating the issue and reply you soon.

Regards,
Domi

Dear Tobias,

 

Thanks again for the error report. We were able to reproduce the bug, started working on it. We will notify you when it is fixed in this topic.

 

regards,

Gabor

Thanks Domi and Gabor.

Much appreciated.

Tobias