make_ndx: 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/make_ndx - from package: gromacs

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

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