Errors on mmff94optimizedstructure command in batch mode

Hi,

I have been trying to calculate the minimized ligand structures by mmff94 forcefield. I have just installed the newest version of Jchem 5.6.0 in linux.

To calculate, I used command "cxcalc mmff94optimizedstructure -f sdf [input file] > [output file] "

However, it gave me java.lang.NullPointerException error...

I have tried similar conformer plugin, lowestenergyconformer, and it worked fine. I thought my ligand file was the problem, so I calculated one of the ligands in GUI mode using MarvinView. Interestingly, mmff94 optimization worked in GUI mode.

I re-installed the Jchem in my home directory, but the mmff94optimizedstructure did not work in command mode...

What is the problem??

Here is the error message I have got.

Error at molecule: 1 ID = 1
java.lang.NullPointerException
java.lang.NullPointerException
        at chemaxon.marvin.modelling.linalg.GradientOptimization.setStorage(GradientOptimization.java:1176)
        at chemaxon.marvin.modelling.linalg.GradientOptimization.addToStorage(GradientOptimization.java:1222)
        at chemaxon.marvin.modelling.linalg.GradientOptimization.store(GradientOptimization.java:1113)
        at chemaxon.marvin.modelling.linalg.GradientOptimization.doStep(GradientOptimization.java:466)
        at chemaxon.marvin.modelling.linalg.GradientOptimization.run(GradientOptimization.java:390)
        at chemaxon.marvin.modelling.mm.mmff94.MMFF94.optimize(MMFF94.java:538)
        at chemaxon.marvin.calculations.ConformerPlugin.calculateMMFF94Structure(ConformerPlugin.java:428)
        at chemaxon.marvin.calculations.ConformerPlugin.run(ConformerPlugin.java:385)
        at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:88)
        at chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit.call(ReusablePluginWorkUnit.java:62)
        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(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)
        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)
Exception in thread "main" java.util.concurrent.ExecutionException: java.lang.NullPointerException
        at chemaxon.marvin.Calculator.outputOnlyPlugin(Calculator.java:1645)
        at chemaxon.marvin.Calculator.consume(Calculator.java:1579)
        at chemaxon.marvin.Calculator.run(Calculator.java:1344)
        at chemaxon.marvin.Calculator.run(Calculator.java:1280)
        at chemaxon.marvin.Calculator.main(Calculator.java:1865)
Caused by: java.lang.NullPointerException
        at chemaxon.marvin.modelling.linalg.GradientOptimization.setStorage(GradientOptimization.java:1176)
        at chemaxon.marvin.modelling.linalg.GradientOptimization.addToStorage(GradientOptimization.java:1222)
        at chemaxon.marvin.modelling.linalg.GradientOptimization.store(GradientOptimization.java:1113)
        at chemaxon.marvin.modelling.linalg.GradientOptimization.doStep(GradientOptimization.java:466)
        at chemaxon.marvin.modelling.linalg.GradientOptimization.run(GradientOptimization.java:390)
        at chemaxon.marvin.modelling.mm.mmff94.MMFF94.optimize(MMFF94.java:538)
        at chemaxon.marvin.calculations.ConformerPlugin.calculateMMFF94Structure(ConformerPlugin.java:428)
        at chemaxon.marvin.calculations.ConformerPlugin.run(ConformerPlugin.java:385)
        at chemaxon.marvin.plugin.concurrent.PluginWorkUnit.call(PluginWorkUnit.java:88)
        at chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit.call(ReusablePluginWorkUnit.java:62)
        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(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at chemaxon.util.concurrent.worker.Worker.run(Worker.java:57)
        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)

Sincerely,

Hi Janghyun,

thank you for the bug report. Can you please attach here the structure that caused this issue?

Thank you,

Sincerely,

Adrian

The first molecule is attached.

I tried again with a single molecule (attached) and it worked fine on command line. But when I ran the mmff94 optimization for the whole compound library, it gave me the error messages.

The first three molecules are in the attached file.

It did not work. It seems that mmff94optimizedstructure does not work when sdf file has more than 1 compound..

Please let me know if this is a bug or my systems are misconfigured. 

Sincerely,

Hi Janghyun,

we could localize a bug based on your error report and on your example molecules.  We are working on the solution. The fix is anticipated to come out in one the of the following releases (5.7 or 5.8).

Sincerely,

Adrian