g_protonate_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 CentOS possible default full paths are:

/usr/bin/g_protonate_d - from package: gromacs

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

On Debian possible default full paths are:

/usr/bin/g_protonate_d - from package: gromacs

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

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