system call issues

[Saurabh Singhvi]

Hi all,

The following code block

foreach $protein (@pdbs) {
       $rmsd[$i] = 0;
       foreach $protein2 (@pdbs2) {
               system("./TMalign $protein $protein2 | cgrep -i rmsd >
temp") == 0 or die $?;
               open(TEMP,'temp') or die $?;
               chomp($line = <TEMP>);
               close TEMP;
               ($length,$rmsd,$tm_score,$id) = split(/\,/,$line);
               $rmsd =~ s/RMSD\=//;
               $rmsd =~ s/\s//g;
               $rmsd[$i] += $rmsd;
       }
       $i++;
}

is giving error :

open: null file name
apparent state: unit 10 named
last format: (A100)
lately reading sequential formatted external IO

Now if i use exec instead of system, things work. But then the code ends
because of exec, and that isn't what i need.

if som1 can plz tell me what the problem is :(

thanks
Saurabh