Well ! That is more or less what i had been doing. These are relelant lines from my CGI script.

`echo -e "$pdbdir\n$pdbdir/$pdbid.new\n" > $pdbdir/hbopt`;
`cd $pdbdir ; $progpath/hbplus/hbplus < $pdbdir/hbopt`;
[download]

i'm writing the required input parameters to the file 'hbopt' in the relevant directory. This file is being created without problems. Then i invoke the script as shown by the second line of code. This program either does not run at all, or does not create output file anywhere. There are no error messages in my apache error logs.