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MarvinSketch (cannot read molecule file)

Hi there,

I've been getting following error while i perform my research on my system using MarvinSketch etc.


Cannot read molecule file.



chemaxon.formats.MolFormatException: Cannot read molecule file.

 at chemaxon.formats.MolInputStream.init(

 at chemaxon.formats.MolInputStream.<init>(

 at chemaxon.formats.MolImporter.init(

 at chemaxon.formats.MolImporter.<init>(




 at chemaxon.marvin.sketch.swing.SketchPanel.fileOpen(

 at chemaxon.marvin.common.swing.MolPanel.openMolfile(

 at chemaxon.marvin.sketch.swing.SketchPanel.setMol(

 at chemaxon.marvin.beans.MSketchPane.setMol(

 at chemaxon.marvin.SketchApplication.bootSketchApplication(

 at chemaxon.marvin.SketchApplication.main0(

 at chemaxon.marvin.SketchApplication.main(

 at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

 at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(

 at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(

 at java.base/java.lang.reflect.Method.invoke(

 at com.exe4j.runtime.LauncherEngine.launch(

 at com.exe4j.runtime.WinLauncher.main(

 at com.install4j.runtime.launcher.WinLauncher.main(

Caused by: chemaxon.formats.MolFormatException: Cannot recognize format by any of the supported molecular file format recognizers.

Unrecognized file contents:

@<TRIPOS>MOLECULE58 60 1SMALLUSER_CHARGES@<TRIPOS>ATOM1 C1 -3.3333 2.6650 0.0000 C.2 1 noname -0.03732 C2 -4.6670 1.8950 0.0000 C.2 1 noname -0.0094...


 at chemaxon.formats.recognizer.RecognitionSubsystem.getFormat(

 at chemaxon.formats.MolInputStream.initTextFormat(

 at chemaxon.formats.MolInputStream.init(

 ... 20 more

How can i solve this type problem? Can you please help?


1 Comment


First of all, I apologize for the late answer. Somehow my system did not show this forum topic. If another issue occur, please open a ticket instead of the forum. To be able to investigate about this issue, I would like to ask you to send the original molecule source if it is not confidential.

Looking forward to your reply,


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