mk_angndx_d: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH

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/mk_angndx_d - from package: gromacs

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