open SAVEERR, ">&STDERR";
open SAVEOUT, ">&STDOUT";
$|=1;
...rest of script...
close STDERR;
open STDERR, ">&main::SAVEERR";
close STDOUT;
open STDOUT, ">&main::SAVEOUT";

##</code><code>##

String[] cmd ={"/home/seaver/MONSTER/monster", "-i" + jobID, filePath + pdbFileName};
        try{
            Process proc = Runtime.getRuntime().exec(cmd);
            BufferedWriter output = new BufferedWriter(new OutputStreamWriter(proc.getOutputStream()));
            BufferedReader input = new BufferedReader(new InputStreamReader(proc.getInputStream()));
            BufferedReader error = new BufferedReader(new InputStreamReader(proc.getErrorStream()));
            output.close();
            input.close();
            error.close();
        }catch (Throwable t){
            t.printStackTrace();
        }