pdb2pqr: 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 Debian possible default full paths are:

/usr/bin/pdb2pqr - from package: pdb2pqr

You may install the required package with command apt-get install {package}

Error in other languages:
pdb2pqr: bevel nie gevind nie
pdb2pqr: comandă negăsită
pdb2pqr: comando não encontrado
pdb2pqr: commande introuvable
pdb2pqr: command not found
pdb2pqr: käsku ei ole
pdb2pqr: không tìm thấy lệnh
pdb2pqr: komanda nerasta
pdb2pqr: Kommando nicht gefunden.
pdb2pqr: kommandot finns inte
pdb2pqr: komut yok
pdb2pqr: nie znaleziono polecenia
pdb2pqr: níor aimsíodh an t-ordú
pdb2pqr: no se encontró la orden
pdb2pqr: no s'ha trobat l'ordre
pdb2pqr: opdracht niet gevonden
pdb2pqr: parancs nem található
pdb2pqr: perintah tidak ditemukan
pdb2pqr: príkaz nenájdený
pdb2pqr: příkaz nenalezen
pdb2pqr: команда не найдена
pdb2pqr: командата не е открита
pdb2pqr: 命令找不到
pdb2pqr: コマンドが見つかりません