prody: command not found

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 CentOS possible default full paths are:

/usr/bin/prody - from package: python2-ProDy

You may install the required package with command yum install {package}

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