You are wonderful. Thanks. I used my original input files and it works correctly. But i will try to learn Text::CSV. I hope i will find some useful examples about Text::CSV on internet. 
my final code:

#!/usr/bin/perl 

use strict;
use warnings;
use diagnostics;


# Open file1 to read
open my $input_file1, '<', "rmsd1.xvg" or die qq{Failed to open "rmsd1
+.xvg" for writing: $!};

# Open file2 to read
open my $input_file2, '<', "rmsd2.xvg" or die qq{Failed to open "rmsd2
+.xvg" for writing: $!};

# Open new file to write
open my $out_file, '>', "rmsd.xvg" or die qq{Failed to open "rmsd.xvg"
+ for writing: $!};

# Copy data from one file to another.

my %file2data;
while(<$input_file2>)
{ 
 next if /(^\s*$)|(^#)|(^@)/;
 my @columns2 = split;
 $file2data{$columns2[0]} = $columns2[1];
}

while(<$input_file1>)
{ 
 next if /(^\s*$)|(^#)|(^@)/;
 my @columns1 = split;
 print $out_file join("\t", $columns1[0],$columns1[1], $file2data{$col
+umns1[0]}), "\n";
}
close($input_file2);
close($input_file1);
close($out_file);

[download]

In reply to Re^4: Adding some columns into a file from two files using perl by perlselami
in thread Adding some columns into a file from two files using perl by perlselami

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.