Please do the following:

  #!/usr/bin/perl
  $pdbfile = $ARGV[0];
  print "path=$ENV{PATH}\n";
  print "procheck $pdbfile 1.0\n";
  #system("procheck $pdbfile 1.0");
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Does $pdbfile contain the value you expect?
Does the path contain the location of procheck?
Are there any spaces in the value of $pdbfile?