....... using warning; first of all , i used that line before ( use strict; use warning;) at the top of my Perl code and for this reason I omit them. I think i should explain a little bit about my code. I have to m file (from matlab) and I just want to make them work automate as a software. I am very very new into Perl. For this reason I used linux shell commands and it worked fine. Now , There is problem with my code.

.... File name argument I will put my file name in the correct place , thank you.

..... substitution operation without something to substitute As i mentioned before, I have two files each of them has spciefic SOL number which I used grep command to count them and then use it as a variable. $cmd =("grep -e HW1 myhalf1.pdb | wc -l > text1.txt") ; open FILE, "<text1.txt"; my $sol1= do {local $/; <FILE>}; print p ("sol1=$sol1"); As you see I have it before. in the code, which you had posted i just omit this line my $sol1 = 'my new stuff'; because i introduce my variable before. and the next line which have $sol1 is remained intact. s{ (SOL) ^\n* }{$1 $sol1}xmsg;

......about errors i ve added the code into my .pl file and run it. After that I check error_log file in the server and there is no warning. I have just changed the line into this my $filename_in = 'topol1.top'; no error.even not making another file. and i ve checked the file permission too.no problem about the permission.

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";
[download]

poj

Dear AnomalousMonk, Yes it worked, and I am so happy. Thank you for your big help. I cant believe that it is solved finally. It is more than one week which I try different solutions and you did it.