autodock4: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/autodock4 - from package: autodock

You may install the required package with command apt-get install {package}
Error in other languages:
autodock4: bevel nie gevind nie
autodock4: comandă negăsită
autodock4: comando não encontrado
autodock4: commande introuvable
autodock4: command not found
autodock4: käsku ei ole
autodock4: không tìm thấy lệnh
autodock4: komanda nerasta
autodock4: Kommando nicht gefunden.
autodock4: kommandot finns inte
autodock4: komut yok
autodock4: nie znaleziono polecenia
autodock4: níor aimsíodh an t-ordú
autodock4: no se encontró la orden
autodock4: no s'ha trobat l'ordre
autodock4: opdracht niet gevonden
autodock4: parancs nem található
autodock4: perintah tidak ditemukan
autodock4: príkaz nenájdený
autodock4: příkaz nenalezen
autodock4: команда не найдена
autodock4: командата не е открита
autodock4: 命令找不到
autodock4: コマンドが見つかりません