#!/usr/bin/perl
use strict;
use warnings;

$_ = '1 AC2 34 TRP A 6 ALA A 7 ILE A 14 GLY A 15';

print join "\n", /\S+(?: \S+){1,2}/g;
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Update: above solution better as:

print "$1\n" while /(\S+(?:\s+\S+){0,2})/g;