matchmol: 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
/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:

/var/lib/wims/other/bin/matchmol - from package: wims
/var/lib/wims/public_html/bin/matchmol - from package: wims

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