Before doing any of this, check if you already have a file named jetbrains-pycharm.desktop in /usr/share/applications/ folder.
If yes, then check which PyCharm version it is related to. If it is related to your older pycharm install, you'll have to create a new .desktop file for PyCharm 5.0. If it is related to the PyCharm 5.0 installation folder, just copy that file to desktop and you're good to go.
If not then you can manually create a .desktop file for PyCharm and copy that to desktop.
Create a .desktop file in /usr/share/applications folder. I'm using nano. You can use gedit or vim or any other text editor.
sudo nano /usr/share/applications/pycharm.desktop
Paste following lines in the file and save it.
[Desktop Entry]
Version=1.0
Type=Application
Name=PyCharm
Icon pathToPyCharmFolder/pycharm-4.5.4/bin/pycharm.png
Exec="pathToPyCharmFolder/pycharm-4.5.4/bin/pycharm.sh" %f
Categories=Development;IDE;
Terminal=false
Your Icon and Exec paths will be different from what I've mentioned.
Copy pycharm.desktop to desktop.
sudo cp /usr/share/applications/pycharm.desktop ~/Desktop/
This must solve your problem.