File::Copy

use File::Copy;

open (my $fh,"<","viewall.pbdid") or die $!;

while (<$fh>) {
    my $from = "/data/pub/pdb/$path";
    my $to = "/tmp/$path";
    copy ($from,$to) or die $!;
}
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This assumes that "viewall.pbdid" only contains file names, not paths with subdirectories. If it does, you'll need to check/create the parent directory under /tmp before copying the file, File::Copy will not create them for you. Check out File::Copy::Recursive and File::Mirror if that is the solution you need.