Could you please adopt a style, any style, for your programs? See perlstyle for some guidance & search around here on the topic.

Problem is that you seem to have data on multiple lines that you are trying to match, but you are reading & matching only one line at a time. Try this ... 

my ( @hydrophobic , @residue );

while ( my $r = <DATA> )
{
  if ( $r=~ m/Hydrophnam_size Center/ .. $r =~ /Hydrophnam_size/ )
  {
    push @hydrophobic , $r;
    next;
  }

  if( $r=~ m/Nligresnam_size Center/ .. $r =~ /Nligresnam_size Print/)
  {
    push @residue , $r;
  }
}

printf "legami idrofobici: %s\n" , join '' , @hydrophobic;

printf "legami idrogeno: %s\n" , join '' , @residue;

__DATA__

...

% Hydrophobic contact

Hydrophname_col
Zero_linewidth W
G Background_col
 189.17  329.15  189.17  317.71  235.30  317.71  235.30  329.15 Pl4
 212.23  323.43 moveto
(Trp 401(A)) Hydrophnam_size Center
(Trp 401(A)) Hydrophnam_size Print

% Hydrophobic contact

Hydrophname_col
Zero_linewidth W
G Background_col
 404.14  338.82  404.14  327.38  450.28  327.38  450.28  338.82 Pl4
 427.21  333.10 moveto
(Val 440(A)) Hydrophnam_size Center
(Val 440(A)) Hydrophnam_size Print

...

% Residue names

gsave
Ligresname_col
 244.91  185.50 moveto
(Atp 1) Ligresname_size Center
(Atp 1) Ligresname_size Print
Nligresname_col
 139.01  612.49 moveto
(Lys 464(A)) Nligresnam_size Center
(Lys 464(A)) Nligresnam_size Print
Nligresname_col
 133.08  424.57 moveto
(Thr 465(A)) Nligresnam_size Center
(Thr 465(A)) Nligresnam_size Print

...

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In reply to Re: problems with pattern match by parv
in thread SOLVED:problems with pattern match by paola82

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