apbs-similarity: 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 CentOS possible default full paths are:

/usr/bin/apbs-similarity - from package: apbs-tools

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