my $i=1;
for my $href(@href) {my $url4= "http://www.ebi.ac.uk$href[$i];
$content=get($url4);
$i=$i+1;
}
}
[download]

for my $param ( @href ){
   my $content = get ( "http://www.ebi.ac.uk$param" );
   process_content ($content); # << This is missing from your code !!!
}

....
sub process_content{
  my $content = shift;
  .. Build HTML tree etc ...

}
[download]

Hi, thanks for your answer, I've tried to modify my code, but it prints only the first two link, I need it to go to these links and then download a file from these links...because I extract the links from the main page, then I ask to go to the links, but I can do it If I have only one, I want to tell to go to the links, and then to download from another links...but I can't make it do repeating my cicle of action...I don't know if my english is good to be understand.... :-( sorry if not, I'm trying to improve also it..I'll paste the code

#!/usr/local/bin/perl
use strict;
use warnings;
use LWP::Simple;


my $url3 = "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum
+/GetPage.pl?pdbcode=2j6p&template=ligands.html&l=1.1";
my $content =get ($url3);

use HTML::TreeBuilder;
my $p = HTML::TreeBuilder->new;
$p->parse_content($content);
my @href;
my $href;
my @anchors = $p->look_down(_tag => q{a});
for my $anchor (@anchors)
    {
      my $txt = $anchor->as_text;  
      if ($txt=~ /EPE\s/)
        {
            print $txt, qq{\n};
            $href = $anchor->attr(q{href});
            print $href, qq{\n};
         chomp ($href);
        push @href, $href;
 #now I need to go to the link where there are my EPE ligand and then 
+parse and extract the link of the RunLigplot.pl that is the output of
+ a program LigPlot, written in perl, is a postcript, and I need that 
+file as a script to extract info....I need to repeat these parsing fo
+r every link,for every EPE.... 
        }
    }
$p->delete;

for my $param ( @href )
    {
    my $content = get ( "http://www.ebi.ac.uk$param" );
    process_content ($content); # << This is missing from your code !!
+!
    }

sub process_content
    {
    my $content = shift;
    $p = HTML::TreeBuilder->new;
    $p->parse_content($content);
    my @href0;
    my @anchors0 = $p->look_down(_tag => q{a});
    for my $anchor0 (@anchors0)
        {
        my $href0 = $anchor0->attr(q{href});
          
        if ($href0=~ /ligplot\d\d_\d\d'/)
        {
            print $href0, qq{\n};
            push @href0, $href0;
        for my $param0 ( @href0 )
            {
              $content = get ( "http://www.ebi.ac.uk$param0" );
                my $content = shift;        
            print my $param0;
            #I need to download files from every link $param0...
my @files = (["http://www.ebi.ac.uk$param0", "$pdb.$param0.pl"],
);  
for my $duplet (@files) {
    mirror($duplet->[0], $duplet->[1]);
}            
            }
    $p->delete;

    }
}
 
 }
[download]

#!/usr/local/bin/perl
use strict;
use warnings;
use LWP::Simple;
use HTML::TreeBuilder;

my $url = "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/
+GetPage.pl?pdbcode=2j6p&template=ligands.html&l=1.1";
my $content =get ($url);

my $p = HTML::TreeBuilder->new;
$p->parse_content($content);
my @hrefs;
my $href;
my @anchors = $p->look_down(_tag => q{a});
for my $anchor (@anchors){
    my $txt = $anchor->as_text;  
    if ($txt=~ /EPE\s/){
        $href = $anchor->attr(q{href});
        push @hrefs, $href;
    }
  }
$p->delete;

for my $href (@hrefs){

  my $url = join(q{}, q{http://www.ebi.ac.uk}, $href);
  print qq{$url\n};
  my $content = get($url);
  
  my $p = HTML::TreeBuilder->new;
  $p->parse_content($content);
  my @anchors = $p->look_down(_tag => q{a});

  for my $anchor (@anchors){
    my $href = $anchor->attr(q{href});
    if ($href =~ /ligplot\d\d_\d\d/){ # e.g. ligplot04_01
      next if $href =~ /pdf/;
      my $url = join(q{}, q{http://www.ebi.ac.uk}, $href);
      print qq{\t$href\n};
      my $content = get($url);
      #print $content;
      # do something with the postscript file
    }
  }
  $p->delete;
}


print qq{done\n};
[download]

In addition to the excellent suggestions you have already received, I thought you might like to see what the errors in your own script are and how to correct them.

This piece of code download the two images you need, at least i hope ;)

#!/usr/bin/perl 
use strict;
use warnings;
use WWW::Mechanize;
$|++;


my $site = 'http://www.ebi.ac.uk';
my $start =
'/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2j6p&templa
+te=ligands.html&l=1.1';
my $img_string = 'ligplot\d{2}_\d{2}';

my $m = WWW::Mechanize->new( autocheck => 1 );
$m->get( $site . $start );

my @links = 
@{ $m->find_all_links( tag => 'a', text_regex => qr/^EPE\s/ ) };

for my $link (@links) {

    print $link->text, "\n", $link->url, "\n";

    $m->follow_link( tag => 'a', text_regex => qr/^EPE\s/ )
      or die "can't follow link";

    my $img = $m->find_link( url_regex => qr/$img_string/ );
    
    $img->url =~ /($img_string)/;
    next unless defined $1; 
    
    print " Fetching $1...",
    $m->mirror( $img->url_abs, $1 )->message, "\n";
}
[download]

hth,
PooLpi