During development it helps to add the following line to your CGI script:

  use CGI::Carp qw( fatalsToBrowser );
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This will, hopefully, cause an error to be sent to your web browser if something went wrong with your script.

Next, the line in your code:

    print $query->('dssp file used is $dssp_file');
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makes me wonder if you didn't mean something like this:

    print $query->p('dssp file used is $dssp_file');
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.. at least ->p() is a function implemented in CGI (it wraps <p>...</p> tags around your text).. I don't know what the behaviour of the ->() call would be from your CGI object $query.

Finally, as holli mentions, you appear to be missing lines of code, not least because I couldn't count 45 lines there to find your error.. or at least look at the 2 or 3 preceeding lines that may have caused the error.

PS: did you add use strict; to your script..

Considered (holli): force insert "Update notification". author changed original content and did not react to a /msg
Unconsidered (holli): Enough keep votes (Keep/Edit/Delete: 6/12/0)