At least run the code before you post it. You have mismatching braces. Maybe what you wanted was something like:

use strict;
use warnings;

my $data = <<IN;
.abc(pqr)
.abc(abc_p)
IN

my $a = qr{ [ .(] }xms;
my $b = qr{  abc | abc_p  }xms;

open my $fh, '<', \$data;

while (my $line = <$fh>) {

    if ($line =~ m{ $a $b }xms) {
        for my $i (1 .. 2) {
            (my $c = $line) =~ s{ ($a $b) }{${1}_$i}xmsg;
            print $c;
        }
    } else {
        print $line;
    }
}
[download]

Prints:

.abc_1(pqr)
.abc_2(pqr)
.abc_1(abc_1_p)
.abc_2(abc_2_p)
[download]

You can now easily use that as a test script to figure out the problem for yourself, unless of course you expect us to do all your work for you? You might like to try some different strings to match - what happens with '.abc' for example, or '27.abc'?

Are a, b and c the best possible variable names? Can you think of names that describe the intent of the variables?