User c23c5e9da4

10-05-2007 02:54:09

We see this error in our logs a lot - I don't have an example molecule to duplicate it however.

java.lang.ArrayIndexOutOfBoundsException: 6

at chemaxon.calculations.pKa.getNitrogenBasicType(

at chemaxon.calculations.pKa.setBasicAtoms(

at chemaxon.calculations.pKa.getApKa(

at chemaxon.calculations.pKa.getAcidicpKa(

at chemaxon.calculations.Ionizer.initMicropk0(

at chemaxon.calculations.Ionizer.calcStartValues(

at chemaxon.calculations.Ionizer.initMsCalculation(

at chemaxon.calculations.Ionizer.calcMicroSpecies(

at chemaxon.calculations.Ionizer.calculatepKa(

at chemaxon.calculations.Ionizer.calculatepKa(


ChemAxon e08c317633

14-05-2007 09:03:54


What version of Marvin/JChem are you running?

Best regards,


User c23c5e9da4

14-05-2007 14:43:53

jchem 3.2.5

ChemAxon 7c2d26e5cf

16-05-2007 19:52:21

Thanks the info. We are checking it.

User 851ac690a0

17-05-2007 08:22:38


From the exception message you have sent it seems to me you are using an older version of JChem.

Are you sure you are using JChem 3.2.5?

This bug has already been fixed, and it should work in JChem 3.2.5. We have tested the pKa module on a large data set, and we haven't got any "ArrayIndexOutOfBoundsException” messages.


User 851ac690a0

17-05-2007 09:10:32


May be the "java.lang.ArrayIndexOutOfBoundsException: 6...." message that you obtained from a logs file was created with an older JChem.

Is it possible?