I installed pycharm normally via bin/pycharm.sh, but the mistake I made was doing bash pycharm.sh while the pycharm directory has inside the D
I managed to solve it. The thing is, Pycharm already installs a launcher inside .local/share/applications. Thus, you need to get rid of it before proceeding to create your own. After that, all you have to do is add your own *.desktop file to the applications directory inside usr/share/applications/.
You need to create your .desktop file using sudo and inside the desktop file:
[Desktop Entry]
Encoding=UTF-8
Name=PyCharm
Exec=/opt/pycharm-3.0.1/bin/pycharm.sh
Icon=/opt/pycharm-3.0.1/bin/pyCharm.png # Changed from pycharm_32.png
Type=Application
Categories=Development;
StartupWMClass=PyCharm
After that is done, you can launch your app properly. Please note that pycharm.sh must also have execution rights.