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
bin/pycharm.sh
bash pycharm.sh
Now the pycharm updated to version 2016.1 and I find the file jetbrains-pycharm.desktop in the path ~/.local/share/applications
jetbrains-pycharm.desktop
~/.local/share/applications
then just edit the path for Icon and Exec
Icon
Exec