When I run that program on these fasta sequences: 

>DROTME_HH_Q02936 
MRHIAHTQRCLSRLTSLVALLLIVLPMVFSPAHSCGPGRGLGRHRARNLY
PLVLKQTIPNLSEYTNSASGPLEGVIRRDSPKFKDLVPNYNRDILFRDE

>DROME_HH_Q02937 
MRHIAHTQRCLSRLTSLVALLLIVLPMVFSPAHSCGPGRGLGRHRARNLY
PLVLKQTIPNLSEYTNSASGPLEGVIRRDSPKFKDLVPNYNRDILFRDEE
GTGADRLMSKRCKEKLNVLAYSVMNEWPGIRLLTTTTTTESWDEDYHHGQ
YEGRAVTIATSDRDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSS
ESLH

>DROME_HH_Q02938 
GTGADRLMSKRCKEKLNVLAYSVMNEWPGIRLLTTTTTTESWDEDYHHGQ
YEGRAVTIATSDRDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSS
ESLH

I get this output: 

Name: >DROME_HH_Q02937 
Number of acidic amino acids:33
Number of basic amino acids:35
Number of neutral amino acids:33

Name: >DROME_HH_Q02938 
Number of acidic amino acids:18
Number of basic amino acids:17
Number of neutral amino acids:18

Name: >DROTME_HH_Q02936 
Number of acidic amino acids:14
Number of basic amino acids:18
Number of neutral amino acids:14

The fasta tags for each protein must be unique.

In reply to Re^3: calculation of charged amino acids by mtmcc
in thread calculation of charged amino acids by yuvraj_ghaly

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