use strict;
use warnings;

my $par_value = 3;

my $inData = <<INDATA;
wire [130 : 0] dgrs_1;
wire [130 : 0] dgrs_2;
wire [130 : 0] mgs_1;
wire [130 : 0] mgs_2;
wire [130 : 0] pqr_1;
wire [130 : 0] pqr_2;
int abc;
int pqr_1;
int pqr_2;
.dgrs_1(dgrs_1);
.dgrs_2(dgrs_2);
.mgs_1(mgs_1);
.mgs_2(mgs_2);
INDATA

open my $in_fh1, '<', \$inData;

while (my $line = <$in_fh1>) {
    if ($line =~ m{ \A (.*dgrs) }xms) {
        print "${1}_$_;\n" for 1 .. $par_value;
    }

    if ($line =~ m{ \A ("\.dgrs") }xms) {
        print "${1}_$_;\n" for 1 .. $par_value;
    }

    if ($line =~ m{ \A (.*mgs) }xms) {
        print "${1}_$_;\n" for 1 .. $par_value;
    }

    if ($line =~ m{ \A (.*pqr) }xms) {
        print "${1}_$_;\n" for 1 .. $par_value;
    } elsif ($line !~ m/(?:dgrs|mgs|pqr)/) {
        print $line;
    }
}
close $in_fh1;
[download]

seems sufficient to reproduce your problem. Check your regular expressions are matching what you expect them to.

I find it impossible to find a mistake since I have no idea what output you were expecting. But anyway: Running the command through the debugger is usually quite useful in such cases:

I am getting output as

.dgrs(dgrs_1;
.dgrs(dgrs_2;
.dgrs(dgrs_3;
.mgs(mgs_1;
.mgs(mgs_2;
.mgs(mgs_3;
[download]

But expected output should be

dgrs_1(dgrs_1);
.dgrs_2(dgrs_2);
.dgrs_3(dgrs_3);
.mgs_1(mgs_1);
.mgs_2(mgs_2);
.mgs_3(mgs_3);
[download]

I know what I mean. Why don't you?

Optimising for fewest key strokes only makes sense transmitting to Pluto or beyond

fyi, this was posted (just as badly) on StackOverflow. No mention of crossposting.