Try

#!/usr/bin/perl
use strict; 
use warnings; 

my $filename_pdb = 'myhalf1.pdb';
my $filename_in  = "topol1.top"; 
my $filename_out = "$filename_in.new"; 

open my $fh_pdb, '<', $filename_pdb 
     or die "opening '$filename_pdb': $!";

my $sol1 = grep /HW1/,<$fh_pdb>;
close $fh_pdb; 
print "\$sol1 = $sol1\n";

open my $fh_in, '<', $filename_in 
     or die "opening '$filename_in': $!"; 

open my $fh_out, '>', $filename_out 
     or die "opening '$filename_out': $!"; 

print "processing '$filename_in' \n"; 
my $count = 0;
while (<$fh_in>) { 
  if ( s/SOL .*/SOL $sol1/g ){ # change as required 
    ++$count;
  }
  print $fh_out $_; 
} 
close $fh_in; 
close $fh_out;
print "$count lines changed\n";
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