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I installed Cisco packet tracer Student 6.2 version on Ubuntu 14.04. When I run "PacketTracer6" in /usr/local/bin/PacketTracer6Student/bin/ application works properly. When I run .desktop file on desktop it opens as normal. But when I create a small network using generic PCs and switch bulbs do change its color to green. What is the problem here? and how to correct it.

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If i understood, when you connect the computer to the switch through straight cable the indicator light does not turn to green on the switch.

Simply because your account doesn't have full access to the PT shortcut on your desktop unlike if opened from terminal with sudo which has (admin privilige) it will work straight away.

So Please do the following,

chmod -R 777 /Your/File/Path

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