Try copying the src/primer3_config file from the primer3 build directory to /opt/primer3_config - it should look in there by default according to the docs (http://www.mcardle.wisc.edu/mprime/help/primer3/primer3_manual.htm)
Re^6: Primer3 - BioPerl
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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