User d664bc87ea
10-11-2012 14:49:12
./marvinbeans/bin/cxcalc 'CC(=O)NC1=CC=C(C=C1)C1=C(C#N)C(N)=NC2=C1CC1=C2C=CC(O)=C1' averagemicrospeciescharge
CC(=O)NC1=CC=C(C=C1)C1=C(C#N)C(N)=NC2=C1CC1=C2C=CC(O)=C1 1
"java.lang.ArrayIndexOutOfBoundsException: 0
at chemaxon.calculations.pka.AcidicPKa.getIonizedSideInc(AcidicPKa.java:2188)
at chemaxon.calculations.pka.AcidicPKa.getOHAcidicpKa(AcidicPKa.java:1860)
at chemaxon.calculations.pka.AcidicPKa.getAlcoholicAcidicpKa(AcidicPKa.java:89)
at chemaxon.calculations.pka.AcidicPKa.calculate(AcidicPKa.java:72)
at chemaxon.calculations.pka.IntrinsicIonization.getApKa(IntrinsicIonization.java:782)
at chemaxon.calculations.pka.IntrinsicIonization.getAcidicpKa(IntrinsicIonization.java:246)
at chemaxon.calculations.pka.PKaLargeModel.getProteinMicropka(PKaLargeModel.java:1863)
at chemaxon.calculations.pka.PKaLargeModel.calcProteinMicropKa(PKaLargeModel.java:1644)
at chemaxon.calculations.pka.PKaLargeModel.calcMicropKa(PKaLargeModel.java:888)
at chemaxon.calculations.pka.PKaLargeModel.reCalcAtomSet(PKaLargeModel.java:606)
at chemaxon.calculations.pka.PKaLargeModel.calcProteinIonization(PKaLargeModel.java:456)
at chemaxon.calculations.pka.PKaLargeModel.calcMacropKa(PKaLargeModel.java:2458)
at chemaxon.calculations.pka.PKaLargeModel.calcChargepHDist(PKaLargeModel.java:3052)
at chemaxon.calculations.pka.PKaLargeModel.calcIsoelectricPoint(PKaLargeModel.java:3229)
at chemaxon.marvin.calculations.IsoelectricPointPlugin.run(IsoelectricPointPlugin.java:276)
at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:88)
at chemaxon.util.concurrent.marvin.CompositeWorkUnit.call(CompositeWorkUnit.java:70)
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.process(InputOrderedWorkUnitProcessor.java:59)
at chemaxon.util.concurrent.processors.InputOrderedWorkUnitProcessor.processInput(InputOrderedWorkUnitProcessor.java:51)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work0(WorkUnitWorker.java:51)
at chemaxon.util.concurrent.processors.WorkUnitWorker.work(WorkUnitWorker.java:36)
at chemaxon.util.concurrent.worker.Worker$1.call(Worker.java:45)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)
"
id Charge
1 averagemicrospeciescharge:FAILED
some SMILES that also fail:
CC(=O)NC1=CC=C(C=C1)C1=C(C#N)C(N)=NC2=C1CC1=C2C=CC(O)=C1
C12C3C=CC(=CC=3CC=1C(=C(C#N)C(N)=N2)C1=CC=C(CO)O1)O
C1(=C(C#N)C(N)=NC2C3=C(C(=CC=C3)O)CC=21)C1C(C)=NNC=1C
cxcalc version: 5.11.3