User 677b9c22ff

29-08-2013 21:01:22


the H-NMR predictor fails with MKXZASYAUGDDCJ-JQHSSLGASA-N:



Clean failed.
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at chemaxon.calculations.ui.nmr.NMRPredictionSettings.applySettings(NMRPredictionSettings.java:629)
        at chemaxon.calculations.ui.nmr.result.NMRResultView.setSpectrum(NMRResultView.java:357)
        at chemaxon.calculations.ui.nmr.NMRPrediction$4.run(NMRPrediction.java:252)
        at java.awt.event.InvocationEvent.dispatch(Unknown Source)
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
        at java.awt.EventQueue.access$200(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)

I recommend to run the whole Pubchem against HNMR and CNMR with

cxcalc hnmr all-pubchem.sdf >all-pubchem-nmr.jdx

I was running only a couple of thousands strucs and I got a couple of failures, mostly/many also with cleaning errors.




ChemAxon 60613ab728

30-08-2013 09:09:35

Hi Tobias,

Thank you for your error report.

The first molecule is a sequence containing atom list and R group, and it seems that there are additional problems with expanding it.
As a workaround, you may try to give explicite molecules as an input in order to eliminate these sort of problems.


For the second molecule (InChi), the C-NMR and the H-NMR works for me. Could you please which version do you use?

But there is a problem with the 3D Clean of the molecule that I could reproduce.
For this particular molecule with the given stereocenters, it is not possible to generate a 3D structure. You can use the stereoisomer plugin to study the problem as it is shown.
There are combination of the signed stereocenters (please find a screenshot attached), which has no corresponding 3D structures. And that is the reason why Clean 3D fails on these particular combinations of stereocenters.

I note that there are two S,S,S structures generated, which only differ in the conformation of the cyclohexane ring. This is a minor bug. Here only one S,S,S structure should be present. The enantiomer R,R,R shows only the chair conformation.

Best regards,


User 677b9c22ff

01-09-2013 18:07:59

Hi Miklos,

all my NMR errors reported are from Msketch 5.11 and the integrated NMR version,

plus Java 7. So maybe these errors are all closed in the newer version which is 6 or higher?

As usual I follow rule, never change a running system, but maybe its time to update again.