Error when the code is converted to runtime jar while using java reflection

When I run my code in Eclipse, it runs smoothly. When I run it as a runnable jar file I get the following error. The code reads a string and performs a certain action if a particular substring is parsed. No external libraries are used to do this. The code runs perfectly when run on Eclipse.

    Exception in thread "main" java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.RuntimeException: Unrecognised token /
        at soft.globulation.proteinParser$SubParser.parse(proteinParser.java:82)
        at soft.globulation.proteinParser.getproteinFromString(proteinParser.java:61)
        at asimov.players.iravan.donkey.RobustDynamicoptimization.getConstantprotein(RobustDynamicoptimization.java:242)
        at asimov.players.iravan.donkey.RobustDynamicoptimization.setup(RobustDynamicoptimization.java:97)
        at bio.globulator.setup(globulator.java:80)
        at bio.simple.Simpleglobulator.setup(Simpleglobulator.java:65)
        at bio.glabulutionState.setup(glabulutionState.java:391)
        at bio.simple.SimpleglabulutionState.startFresh(SimpleglabulutionState.java:49)
        at bio.glabulutionState.run(glabulutionState.java:438)
        at bio.glabulve.main(glabulve.java:769)