I edited your script and used <code></code> tags---never leave home without them:). 
#!/usr/bin/perl -l

use strict;
use warnings;

my(@lines) = '/tmp/zea_mays.txt';
my $log   = '/tmp/zea_mays.log';

die $! unless open IN,  '<', @lines;
die $! unless open OUT, '>', $log;

my $peptides;
my $seq;
my $flag = 0;
while ( defined( my $line = readline \*IN ) ) {
    do {
        foreach $line (@lines) {
            chomp $line;
            if ( $line =~ /^>/ ) {
                next if $flag > 0;
                print "\n";
                print OUT "$line";
            }
            else {
                $line =~ s/\s//g;
                my (@peptides) = split( /(?<=RK(?!P))/, $line );
                print OUT "@peptides";
            }
        }
    };
}
close IN;
close OUT;

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In reply to Re: First header missing from FASTA data by Khen1950fx
in thread First header missing from FASTA data by bugiep

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