Hi Sandeep,
I have moved the toptic to the "License issues" section.
You can find the license installation instructions here:
http://www.chemaxon.com/marvin/help/licensedoc/install.html
Please note that there are multiple instructions, depending on the way of usage (desktop GUI, server applications, etc), and the user executing the application is also relevant.
I am a bit confused here. I can use the member functions of TopologyAnalyserPluginTopologyAnalyserPlugin class (eg bondCount) using cxcalc. Therefore I am not sure why I have problem with the license file.
Certain calculations may be allowed free wihtout a license.
Chemical Terms expressions ("evaluate", Evaluator class) use many of the same calculations.
There is a nice tabe for Cehmical Terms showing all calculations and their licenses.
As you can see a simple bondCount does not need a license:
http://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html#bondcountex
Usually it's the easiest to check installed licenses via running License Manager ("licenese") with the same user as executing the Java program.
If you cannot solve the problem, please locate and send us the license file to our technical support e-mail address listed here:
http://www.chemaxon.com/contact-us/
The location os the license file is usally listed in the stack trace.
Please paste the full stack trace too, as well your exact JChem version.
Best regards,
Szilard