#! /usr/bin/perl -w
open AA, '<',"A.txt"    or die "open: $!";
   foreach $line(<AA>)
   {
       chomp($line);
       @temp=split(/\./,$line);
       $new=$temp[0].'.'.$temp[1];
open BB, '<',"B.out"    or die "Failed to open B.out: $!";
       foreach $line1(<BB>)
       {
         @temp1=split(/\s+/,$line1);
         if($new eq $temp1[0])
           {
           print $temp1[1]."\t";
           print $temp1[2]."\n";
           }
       }
close (BB);
}
close(AA);

##</code><code>##

A.txt
1a6m_-.ent.dssp
b1b5e_A.ent.dssp
b1bx4_A.ent.dssp
b1bx7_-.ent.dssp
b1bxy_A.ent.dssp

##</code><code>##

B.out
b1a6m_-.ent  79K  83E 127.119
b1a6m_-.ent  80G  84A 136.545
b1b5e_A.ent 123R 127M 132.48
b1bx4_A.ent  61H  65S 145.4

##</code><code>##

 
 @temp1=split(/\s+/,$line1);

##</code><code>##

 @temp1=split(/ +/,$line1);