Something like this should work (file is a text file containing all the fasta sequences): 

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

my $file = $ARGV[0];

my @currentProtein;
my %protein;

open (FASTA, "<", $file) || die "Can't open $file\n";
my $fastaLine; 

my $protSequence;


while (<FASTA>) 

  {
    #print STDERR "$_";
    chomp;
    if (($_ !~ /^>/) && ($_ =~ /\w/)) 
      {
        push (@currentProtein, $_);
      }
    if (/^>/) 
      {
          $fastaLine = $_;
      }

    if ((($_ !~ /\w/) || (eof)) && (@currentProtein > 0))
      {
        $protSequence = join("", @currentProtein);
        
        $protein{$fastaLine} = $protSequence;
        @currentProtein = ();
      }
   
    }
close FASTA;
foreach my $key (sort(keys %protein)) 
    {
      my $count_of_acidic = 0;
      my $count_of_basic = 0;
      my $count_of_neutral = 0;
      my $aa;
      my $sequence = "$protein{$key}";
      $sequence =~ s/\s//g;
      my @prot=split("",$sequence); #splits string into an array
      #print " \nThe original PROTEIN file is:\n$sequence \n";

      while(@prot)
        {
          $aa = shift (@prot);
          if($aa =~/[DNEQ]/ig)
            {
              $count_of_acidic++;
            }
          if($aa=~/[KRH]/ig)
            {
               $count_of_basic++;
            }
          if($aa=~/[DNEQKRH]/ig)
            {
              $count_of_neutral++;
            }
      }
      print "\nName: $key\n";
      print "Number of acidic amino acids:".$count_of_acidic."\n";
      print "Number of basic amino acids:".$count_of_basic."\n";
      print "Number of neutral amino acids:".$count_of_neutral."\n";
    }

[download]

I hope that helps.

In reply to Re: calculation of charged amino acids by mtmcc
in thread calculation of charged amino acids by yuvraj_ghaly

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