pdb2gmx_d: 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/pdb2gmx_d - from package: gromacs

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

Error in other languages:
pdb2gmx_d: bevel nie gevind nie
pdb2gmx_d: comandă negăsită
pdb2gmx_d: comando não encontrado
pdb2gmx_d: commande introuvable
pdb2gmx_d: command not found
pdb2gmx_d: käsku ei ole
pdb2gmx_d: không tìm thấy lệnh
pdb2gmx_d: komanda nerasta
pdb2gmx_d: Kommando nicht gefunden.
pdb2gmx_d: kommandot finns inte
pdb2gmx_d: komut yok
pdb2gmx_d: nie znaleziono polecenia
pdb2gmx_d: níor aimsíodh an t-ordú
pdb2gmx_d: no se encontró la orden
pdb2gmx_d: no s'ha trobat l'ordre
pdb2gmx_d: opdracht niet gevonden
pdb2gmx_d: parancs nem található
pdb2gmx_d: perintah tidak ditemukan
pdb2gmx_d: príkaz nenájdený
pdb2gmx_d: příkaz nenalezen
pdb2gmx_d: команда не найдена
pdb2gmx_d: командата не е открита
pdb2gmx_d: 命令找不到
pdb2gmx_d: コマンドが見つかりません