will the code look like this? after embedding the external script ?

#!/usr/bin/perl

use strict;
use warnings;


my $dir = '.';

#for embeding the mcsearch percompile version
my $mcsearch = '/bin/mcsearch';

#to read the PDB files from the directory
opendir DIR, $dir or die "Cannot open directory $dir:$!\n";

my @pdb_files = grep { -f $_ && $_ =~ /\.pdb$/ } readdir DIR;

closedir DIR;

print "Enter the script file";
$a=<>;

open(IN,$a) or die;


#giving each file as a input to mcsearch
for my $file (@pdb_files)

 {
while(<>)

{
    my $content = `$mcsearch "$dir/$file"`;

    chomp $content;

    print "Content of $file is $content\n";

}
}

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