You will find that it helps a lot if you provide a code sample demonstrating your problem. I know what I mean. Why don't you? will give you some ideas for how to crunch your actual code down to a useful sample. However, consider:

use strict;
use warnings;

my $info = <<INFO;
PDB ID,SITE NUMBER,RESIDUE TYPE,CHAIN ID,RESIDUE NUMBER,CHEMICAL FUNCT
+ION,EVIDENCE TYPE,LITERATURE ENTRY
102l,0,ASP,,20,S,PSIBLAST,206l
103l,0,ASP,,20,S,PSIBLAST,206l
104l,0,ASP,A,20,S,PSIBLAST,206l
104l,1,GLU,B,11,S,PSIBLAST,206l
INFO

my %lookup;
<DATA>; # Skip the header line

while (<DATA>) {
    my ($key) = split /,/, $_, 2;
    $lookup{$key} = 0;
}

open my $InFile, '<', \$info or die "Failed top open menory file: $!";
+;

<$InFile>; # Skip Header

while (<$InFile>) {
    my ($key) = split /,/, $_, 2;
    
    next unless exists $lookup{$key};
    ++$lookup{$key};
}

close $InFile;

for my $key (sort keys %lookup) {
    print "$key: $lookup{$key}\n";
}

__DATA__
PDB ID,SITE NUMBER,RESIDUE TYPE,CHAIN ID,RESIDUE NUMBER,CHEMICAL FUNCT
+ION,EVIDENCE TYPE,LITERATURE ENTRY
102l,0,GLU,,11,S,PSIBLAST,206l
103l,0,GLU,,11,S,PSIBLAST,206l
104l,0,GLU,A,11,S,PSIBLAST,206l
[download]

Prints:

102l: 1
103l: 1
104l: 2
[download]

Ah, it's been pointed out that I do in fact have a typo in my code:

In line 9, change "$indices{$line}" to "$indices{$key}".

I'll update my previous post to fix the code.