obrotamer: 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 CentOS possible default full paths are:

/usr/bin/obrotamer - from package: openbabel

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

On Debian possible default full paths are:

/usr/bin/obrotamer - from package: openbabel
/usr/lib/debug/usr/bin/obrotamer - from package: openbabel-dbg

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