I know its more than a year since the question is posted. Had to deal with the same problem and could solve using the below method. Thought of posting it, if it would be useful for anyone else. Thanks !!

specify the PRIMER_THERMODYNAMIC_PARAMETERS_PATH in the input file for the primer3_core software 

cat inputfile.txt



SEQUENCE_ID=example
SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAG
+CACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
PRIMER_TASK=generic
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-100
P3_FILE_FLAG=1
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/home/User/Softwares/primer3-2.3.
+5/src/primer3_config/
=

[download]
Thanks, Tinu

In reply to Re^7: Primer3 - BioPerl by tinu329
in thread Primer3 - BioPerl by blarsen20

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